I can't answer your question with certainty. No, there doesn't seem to be anything off about writing, production, or art direction in the last episode:
- The last 3 episodes were all written by the same person, 影山由美 (kageyama yumi). 影山由美 was in charge of series organization/composition and wrote more episodes then anyone else.
- The Producer, 山吉康夫, also produced episodes 3, 9, 15, 20, 26, 32, 37, 42, 46, and of course 51.
- Art direction was performed by 馬越嘉彦 (umakoshi yoshihito), who was actually in charge of character design for the whole show. He also provided art direction for episodes 1, 16, 25, 32, 43, and of course 51.
This is all from the wikipedia page on the anime, which lists all the details by episode: 花より男子 アニメ TVシリーズ
I've seen the whole anime, have read the manga all the way through a couple of times, and watched two of the live actions (Japanese and Korean), I was really into Hana Yori Dango back in the day. I felt like the end of the anime was unexpected/unforeseen and that they just rushed an ending together. The show did a pretty good job of following the manga ... right until those last few episodes/last episode. My guess is they were told,
were cutting the show, end it.
so they did and things didn't turn out quite the same as usual.
According to HMV Online, the average rating for the TV show was 9.9%, max was 12.1%. I don't know much about TV ratings, but the Japanese TV Drama was never lower then 17% in season 1 and 19% in season 2 (same Wikipedia page). To me this looks like a cut due to ratings.