Medaka Box got way better in Abnormal, and I'm super hyped about any third season that may happen.

Sket Dance, Bakuman, Queen's Blade, Project K

One Piece, Code Geass

K is only 1 season. Also, it's K or K Project, not Project K.

Yeah generally the manga material gets better as it goes along in my opinion, so the anime should follow suit as well.

...

FMA brotherhood kind of qualifies for this. Not that the first part of the show is bad per se, but most of it is spent covering the parts of the canon plot that were covered in the original FMA series. By that I mean the parts before the studio created plot was adapted to finish the series. As such it wasn't treated with as much detail and care as it was in the first series, as they were trying to strike a balance between telling the complete story, and not dragging it out to much for folks who watched the original and wanted to see animated what happens after the already covered material. When it finally does get to the new material the entertainment value jumps up considerably.

I'd say Clannad: After Story is a good example. The Fuko arc can go **** itself.

Dragonball I felt picked up significantly as it went along. The first couple of seasons in particular I didn't love, too silly and inane. Around the time Demon Lord Piccolo shows up things are pretty badass and more in line with what DBZ became.

But, but, but I liked fuko
But yeah after story was better

Code Geass and Rosario + Vampire

That's a tough one, although I have a few the first one that came to mind would be Fighting Spirit.

Yah sorry about that

I saw the preview of the second season when I was visting TV Tokyo with my cousin (he works there) and there is a much more cohernt plot from what I see in the storyboards.

Oh. thanks ^^ seems interesting! Gonna give it a try.

Defo One Piece

D.Gray-man
Gensomaden Saiyuki
Code Geass
X/1999 (only watch this is you like watching REALLY sad animes, after all it's CLAMP)
FMA
Fate/Zero (if you don't think there are 2 seasons go to episode 14 here on CR, it says very clearly season 2)

Too many to list, so I'll just give the recent ones. Medaka Box Abnormal, Haganai NEXT, Seitokai no Ichizon Lv. 2 (arguable), Minami-ke Tadaima, and Jormungand Perfect Order. I find that, as you get further into a show, if it's decent, you'll get to know the characters better, and through multiple seasons, gain a sort of attachment that is difficult to achieve in 1 season's time (although it's certainly not impossible) most good shows get better over time -- not necessarily because the writing is better, but because the characters have a little more depth to them. In real life, I've found that hanging out with and talking more with people I'm not initially fond of lets me understand them better, and at the very least, gain a tolerance. I feel like it's pretty much the same concept with fiction. (Although like real life, if I really just don't want to talk to you, I won't. If I really don't feel like putting up with a character, I won't -- lots of similarities I guess).

Naruto or Bleach are really not all that great, but as you spend time watching the characters do stuff, you tend to get used to them -- perhaps even garnering a certain fondness for someone as annoying as Naruto. Soon enough, you find yourself happily (although disappointingly) tuning in to fillers every week just because you reckon you'll still have a decent time hanging out with some characters you haven't seen in a couple of weeks. So I actually hold the (perhaps) radical idea that later seasons are usually just as enjoyable as their first, if not more.

One Piece
Was good at the start imo, got better and better. But after the timeskip it went more and more downhill, BUT not drastically at first. The last 10 or so episodes have been annoying, becaus of so much dragging the scenes out and such.