Here's a list I made for the things skipped/changed from the manga to the anime:
(not including filler and some obviously adaption changes)
- Some Death Note references were deleted.
- In Moritaka and Akito discussion, Iwase were mentioned being dumb, in the anime it got cut.
- Some scenes of Moritaka and Aktio talking about boxing were cut.
- Introducing his uncle principles for manga, Moritaka referring to "Qualification of a man" and it's principles before his uncle's. In the anime it got cut straight to his uncle's.
- Moritaka and Miho's “goodbye” were for freaking 30 minutes. The anime “made” it shorter.
- In the manga Moritaka and Miho got distracted by passing schoolgirls. In the anime by some random dog.
- In the manga, Moritaka scattering the storyboards over the river. In the anime they also tearing the storyboards apart.
- In the manga, when Moritaka scattering the storyboards, Aktio commenting about the environment groups might see them, and running away. In the anime, someone who passed there telling them it's bad for the environment and they collecting it.
- The anime censored and changed some parts of the discussion about Miho's failing auditions.
- After Miho debut on TV Moritaka analyse her performance. In the anime he got encouraged by it.
- In the manga, Miho and Moritaka talking over the phone when Kaya giving him Akito's cellphone. In the anime, Miho closing the call on Moritaka. (and they'r having their first phone call talk only on episode 25)
- Where in the anime the serialisation meeting is getting introduced in this episode, in the manga it got introduced much earlier, while it get more expanding in the meeting of this episode.
- Akira and Yuujiro are talking about editors changes. Got cut in the anime.
- Christmas eve scene were cut in the anime.
- Koji makes an appearance in the New Year Party. Got cut in the anime.
- Miho's side story is starting differently in the anime than the manga as it starts much earlier in the manga, though its climax is on the right timeline.
- Hiramaru scenes taking different timeline in the anime.
- Akito talking to Miho got cut in the anime. And also scenes of Miho with her mother.
- Miho talking to Moritaka's mother got cut in the anime.
- Moritaka has a talk with his hospital room partner. Got cut in the anime.
- Extra information about TRAP ending were cut in the anime.
- Ryo Shizuka character removed from the anime.
- In the manga Akito forget Iwase's novel in the studio, and then Moritaka putting it in the shelf. In the anime Akito is the one putting it there.
- Fukuda and Ko character development cut out in the anime. Hiramaru scenes as well.
- Obvious scenes were censored in the anime.
- Hiramaru's "plan" had been changed in the anime.
- Where the manga had extended on Moritaka's uncle, the anime shortened it.
- Where the manga had been on Akito and Kaya moving, the anime cut and censored part of that.
- Eiji to appear on TV had foreshadowing in the manga. Got cut in the manga.
- Hattori is threatening Miura telling Moritaka and Akito about Eiji getting +Natural anime adaption. The anime cut it through to the point where Miura is telling them.
- When Moritaka getting home after Eiji appears on TV, he don't have his own cellphone with him to cal Miho so he takes the home phone. In the anime he have his own cellphone with him.
- Moritaka and Miho discussion is much extended with character development. The anime cut it through the character development.
- The anime had changed the order of the events of the manga, causing some changes in the stories.
- The taxi joke were cut out in the anime.
- Christmas eve in the manga and the Serialisation meeting day are completely separated days. The anime made them the same day.
- When Moritaka showing his uncle grave the results for PCP he saying that his uncle would probably say that the challenge only just began and such. In the anime, his uncle "ghost" actually appears and saying that.
- In the manga, after Hattori getting to edit PCP he's thinking himself being selfish so he goes to the editor-in-chief, in that event the editor-in-chief tells him the condition for PCP to keep ongoing. In the anime, those two events aren't related to each other, and Hattori doesn't go to the editor-in-chief when thinking he's selfish.
S3 (this is where the most changes were made)
- Moritaka and Miho on the train have exactly 2 to 3 frames in the manga to justify the "time flows fast when we happy" idea. The anime made it longer.
- While in the manga Shiratori have lots of dogs, in the anime he have only one.
- Mashiro and Aktio character development were cut from the anime.
- Moriya story and development got cut in the anime.
- Shiratori arc - shortened in the anime.
- Mashiro development got cut in the anime.
- Super Readers Love Fest arc in the manga (vol13) got cut through and shortened in the anime.
- In the manga, Maoritaka and Akito are hiding from Kaya that PCP won't get anime, so when they discussed about Akito making Lavuta they mentioned that PCP won't get anime with Kaya listening and among the lines of the manga Kaya is surprised by it. The anime didn't let any of these being significant.
- Furthermore to that, Kaya and Miho talking about Moritaka and Akito about PCP not getting anime had been removed from the anime.
- That and along more developments the Super Readers Love Fest arc had in the manga, had been cut roughly in the anime.
- Moritaka and Akito discussion after the result of the Super Readers Love Fest have more "meat" and development on the manga. Where in the anime it got cut like most of this arc development.
- The award ceremony was in the manga after Hiramaru and Ko story. The anime rotated it to before their story. And so a scene from Nonamine arc as well.
- Where the manga extended the award ceremony, the anime made it a rough 1 minute.
- The manga "Classroom of truth" have more pages in the manga, and also its final page have been cut in the anime. And also more commentary of Moritaka and Akito on the "Classroom of truth" been cut in the anime.
- Flashback from 'Nonamine return arc' were rotated to this episode.
- Kosugi had more fist fight with Nonamine in the manga, and also threatened him to call the police. The anime cut it and censored it.
- Mortiaka and Akito meeting Nonamine in the New Year Party has little changes, and Nonamine's line in the manga that he's going to beat them with "brand new method" were cut in the anime.
- Parts of the New Year Party got cut in the anime, mainly due the 2-chapters arc of Nakai.
- In the manga, Akito telling Moritaka that he had a crush in second grade on Ichiko, and Moritaka meeting her in the reunion. In the anime that part with Akito got cut, and when Moritaka meets her in the anime he says "So this is Ichiko, huh?" without any relation.
- In the manga Moritaka learning to drive mentioned much earlier in the manga. In the anime only in this episode it being mentioned for a line.
- In the manga, Yamashita arriving to the reunion later. In the anime he's been there already.
- In the manga at Moritaka and Akito discussion when Akito mentioning Ashite No Joe they are adapting lines from that manga to their situation. In the anime it got cut through the end of their discussion.
- 2-chapters arc of Nakai got cut roughly and changed heavily in the anime. Grand changes from the manga: 1. Moritaka part in this arc 2. Longer fist fight of Hiramaru vs Nakai 3. Fukuda part in the fist fight 4. In the manga Ko threatens to call the police and actually intends too, but ended in calling Fukuda, so no police really involves. In the anime, at the end of Nakai part there's police sirens. 5 Hiramaru making Friend with Nakai changed heavily in the anime too.
- This 2-chapter arc were after the Nonamine arc in the manga before the reunion, to make a point by connecting it. The manga delayed it after that.
- In the manga, when Eiji asking Yuujiro about the differences in votes between 2nd place and 1st place, he's reading PCP. In the anime he's reading his Crow manga. The scene in the anime also combining another scene from the manga as following the next change.
- In the manga, Eiji shouting about he can't make a storyboard for Crow, when asked by Yuujiro he's saying it's because his names are usual in 2nd place and he wants 1st place. In the anime Eiji only stating that the next one going to be in 1st so he will be delayed.
- The 'Copycat arc' in the manga is 3 chapters long. the anime crammed it all to single episode cutting several Akito, Hattori and as well Ashirogi Muto development from the manga. (some big, and some that not necessarily big development but mostly cutting lines that highlighting those developments)
- In the manga, when Moritaka comes to Akito's work room they'r talking about the solution for next chapter. In the anime, the understanding between them is in the air.
- In the manga, when Yoshide coming to Hiramaru's house he have face mask. In the anime, for comical purposes he have full oxygen tank.
- Some trial and error of Moritaka and Akito in the manga changed in the anime, like Kaya commenting about making code out of rainbow, in the manga it wasn't treated while in the anime it made them hint. Some was cut as well.
- 'Nonamine return' arc (end of vol16-vol17) had been removed in the anime. (And so all the development had been done in character and plot)
- Regarding the arc removed from the anime, connection from the arc to the new manga of Ashirogi Muto has been removed as well.
- Extra details on Zombie Gun story had been cut in the anime.
- In the manga when Moritaka making the manuscript for Reversi it's being showed he's completely exhausted. In the anime he's completely normal.
- In the manga, when Hattori and Yuujiro are in the bar, Hattori is completely drunk. The anime censored it.
- Extra details on PCP moving to Heishuu Jump were cut in the anime.
- The part of Moritaka and his grandpa has been shortened in the anime. (some were rotated to Episode 23)
- Some very little Moritaka development were cut on the anime. And so some of Obata's faces for Mashiro were cut too.
- Some extra details, and also Akito development were cut from the anime too.
- In the manga, in the flashback of Hiramaru he's showing shaking as he usually does. In the anime they changed him to look normal and formal.
- In the manga, Yoshida thinks for Hiramaru's sake is more extend and have some of his own backgrounds (and some gag from the editorial department as well). In the anime it got cut and in the same occasion he's thinking about Hiramaru he's going to his place to encourage him.
- Some of "Proposal Mission" in the manga got cut in the anime.
- In the manga, Hiramaru and Ko are riding the ferris wheel three times, and Hiramaru proposing to Ko in the second on when Ko noticed while riding that Yoshida is there, after that they getting on the ferris wheel another time with Ko asking the operator. In the anime they changed it to 2 rides, making the 2nd like the 3rd in the anime.
- In the manga, the reason for Moritaka and Akito going to the Tezuka Award party is pretty much for Kato's request and breather reasons. In the anime their coming is blended with Akito saying "we are not in the mood for the party" without much introduction as the manga.
- Ishizawa part in Miho arc was removed in the anime. And some crazy otaku elements censored as well. (like "Die Ashirogi Muto!")
- Regarding the above, though some net chat are appearing in the anime in this arc, a lot of those got cut in the arc.
- Fukuda part in Miho arc and as well Road Racer Giri radio was removed from the arc.
- Some question in Miho's radio were censored.
- Moritaka's grandpa "agreement" on Moritaka and Miho's marriage was discussed much earlier in the manga (see Episode 18 changes). In the anime it's been here with his mother's agreement.
- In the manga, when Mortiaka's Mother "agrees" to the marriage, Moritaka having classic comical reaction of spitting drink. In the anime he have classical comical reaction of falling.
- In the manga, after Miho's Mistake, the one who found out the script for the audition was the mistaken one was the director. In the anime, the producer is breaking the room to tell them that.
- In the manga, when the auditions ending, some of the actress addressing the man in charge that Ashirogi Muto revealed Miho that the script was wrong for her to get the rule. In the anime, there's some actresses that saying that in the hallway and even not in front of Miho.
- In the manga, the public audition is supposed to be show over a week and then have the result. The anime made it in one day only, changing the events of the manga.
- The anime had moved the prologue from chp175 to after the end, and made kind of it's own prologue.
(though it's seems the anime changed a lot, all those (except S3 probably) are very small parts though still notable, Bakuman anime is pretty faithful to the manga except what it skipped)