Oh yes, plenty of times
As others have said, the Therian formes changed my mind about the trio in gen V... at least about Tornadus and Landorus
I still think Thundurus looks crappy.
I've always disliked Emboar's design, but I had one in my starter in White2 and it was completely useless -.- Once I found out I could have it re-learn Hammer Arm it got a bit better, but I am still scarred from having to play up until the Elite 4 with only Arm Thrust...
I never liked Staraptor, but seeing Unfezant made me really wish for it back
I loathed Bidoof from the moment I set eyes on it (like many others) but I recently bought a sticker book and the one for Bidoof is actually pretty adorable >.<
I disliked Stunky at first but I absolutely hate it since I realized its face was purposely drawn to look like butt cheeks and its cry was made to sound like a fart ._. Really, gamefreak? How ridiculous can you get.
There are others but I won't list every single one...