Warning: This post contains opinions that may disagree with yours. If you are easily offended by differing opinions, I would advise you do not read this post.
So all in all, I liked G2 and was sad to see it go, it offered some great sets with great builds, and here is my opinion on the best and worst sets. Again, THIS IS MY PERSONAL OPINION!
-Best: tie between Lewa and Pohatu
-Worst: Gali all the way (because of the gappy build and the bad mask that made her look like a discount Nokama)
-Worst: Tahu (because of the Hero factory chestplates used for the legs, I really would have added stickers to them (like on Kopaka and Onua's respective parts with stickers)
-Best: I'm going to get a lot of hate for this, but I think it's a tie between Uxar and Ketar
-Worst: Melum (I dislike the arm design and the action feature, after the novelty of Melum only being able to hug stuff wore off)
-Best: Even though he isn't a protector, he still has the protector mask, so I'm going to say Ekimu
-Worst: Protector of Water (his color scheme is to dark to compliment the Gali Master figure, and his legs look out of proportion to me)
Villains (meaning all villain sets ever released in both of G2's years):
-Best: Umarak the Hunter and Skull Warrior
-Worst: Tie between Skull Scorpio (I like the building experience for Scorpio, I just dislike the finished product) and Skull Grinder's Stock build. (the arm friction fix makes me like Skull Grinder just a bit more, but I still don't like it)
Favorite Set/Combo Model overall: Big-kimu (but with the blue Mask of Creation replaced with the golden Mask of Creation)
To be honest, I think that G2 had some pretty solid sets, and for most of these, it was hard for me to pick a favorite set, the "bad" sets were very few and far between in G2. Some people may not like it because it uses "Hero Factory" parts, but I think that it was one of the best years for bionicle's stock sets. They are some of the only sets that I did not disassemble for moc-making purposes.
Please post your own version of this list in the comments, and be sure to say why you disliked the sets you didn't like.