Here are some I was not too insane about until I used them, saw them in action, or saw them in the show:
Marill
Azumarill (it saved me from Flannery in Emerald, and Huge Power made it kick behind on Black 2)
Bulbasaur
Venusaur
Chikorita
Bayleef
Meganium
Zigzagoon
Linoone (again Emerald)
Palkia, despite the obvious
Oshawott (I still am not really fond of Ash's...)
Sigilyph (I hated its guts because it nearly wrecked me on Black, but it has grown on me)
Garbodor
Vanilluxe
Hydreigon (yes, really; I stayed away from it for a while because of Ghetsis, but after my Zweilous on Black evolved, it grew on me rapidly)
Reshiram but I was lying to myself by saying I was more fond of Zekrom, so not really
Zekrom (I got over it being overrated after a while but I never hated or disliked it)
Kyurem (at first I thought it was strange, still do, but not as much)
Keldeo (thank you M15)
Meloetta (at first I thought it was furry bait while it is not)