definitely
season 1! 
It's the best, the original, and I love the casts soooooooooo much more! Especially
OGURI SHUN 
Matsujun, Ishigaki Yuma (Minami), Narimiya Hiroki (Noda)& Waki Tomohiro (Kuma)! I love the storyline more too!
Season 2 was a huge flop for me, it was just a carbon copy of the original, everything was the same, the same deja vu, it was really annoying for me! Yes, even though there were more hot guys in season 2, but that's about the only good thing about it for me, I wasn't interested in any of the guys...not even Kamenashi Kazuya...all the students were so similar to the guys in season 1, whenever I watch them, they just remind me so much of Shin, Uchi, Kuma, Minami Noda, and everyone else from G1, and I just feel like wanting to watch G1 again.
I've only seen G2 once, and I don't intend on watching it again.
season 3 was just slightly better than G2, but still the same old annoying deja vu...I did like like guys in G3 slightly more than G2...but...
season 1 is still the best by far! better story & better casts for me! I watch it everyday!
order of preference:
1. Season 1 (by far!)
2. Season 3
3. Season 2