Just to clarify my main reference is family, namely my brothers and father who have all lived in Japan for years at one time or another time for various reasons.
One of the biggest reasons is their expense. Animes are expensive to make. Anime and video games are the most expensive form of advertising there is for manga, which is the real moneymaker. A single episode can cost anywhere between $100,000-200,000. That's the equivalent, in the current market, to ¥1,0072,000-2,0144,000. This is also an average as it isn't always a set amount, and some anime get more funding than others if they are popular or raised it somehow. So that means for a single 24 episode season you just spent $2,400,000-4,800,000 (which is a lot of yen, you can do the math yourself) on what may be a boom or bust for the company.
Now with the anime out you have to give it time to market your manga for you. If sales don't pick up much or at all after the anime comes out it isn't likely the anime will continue. Like KiaiFighter pointed out the only ones that get a really longstanding season are the ones who have an incredibly long and popular manga, probably through JUMP or one of their competitors. Like he said you have anime like One Piece, Gingtama -- or Fairy Tale through Weekly Shōnen Magazine -- which all feature hundreds of episodes because they were popular and established before the anime even got started and can afford to be given longer seasons. The ones that don't have that kind of backing must wait potentially years for the anime to market the manga and paraphernalia before there is even consideration for a new season.
Then there is also the problem it takes time to make a manga and storyline. Lesser known mangas that don't have the advantage of JUMP or other forms to effectively distribute their manga probably don't have a whole lot of arcs covered. Basically a single 13 episode season can catch up on the whole series effectively. So even if it is popular, the funds are available, and the populace is waiting, it is likely it might very well be delayed anyway for several years simply so the author can get ahead a few arcs. Look at the anime Tsukaima no Zero which had between two to four years between each 12 episode season so that the light novels could get ahead enough (didn't really matter though because the author passed before he could finish but I digress). If they don't then you just have a huge number of filler episodes, like with Naruto and the Hunter x Hunter from the 1990's (I can't get over how the nickname for Hunter x Hunter is Hiatus x Hiatus because the author constantly puts off continuing the manga which was only recently started again. Its been around for almost 20 years but they only have about 150 episodes worth of anime, as opposed to One Piece which started a year before, and even GinTama. But again I digress).
Lastly, like KiaiFighter also pointed out, Dramas are a whole other ballpark and shouldn't be touched with another season because they generally leave everything wrapped up nice and tightly so there shouldn't be any complaints other than the tears of joy a the happy ending or shock and denial for the depressing ending.