Maybe it's all the Anime-related promotions, movies, and fillers that make me feel this way, but the characters aren't the same anymore. I think ever since the time skip started it's all felt a little different…I don't feel this way about the anime up until recently though.
You also need to look at this from a realistic plot and character advancement point. Though it may seem like a lifetime (10 years for us), the Strawhats only spent at most a few months together pre-timeskip. That was the total length of their grand journey. People change; especially within a gap of them being separated for longer than they've known each other. Every Strawhat had their own self-reflective little adventure and matured from it – in a way,they are different people.
Physically, my issue is only with the women of the group, who Oda is drawing more generic than ever - especially Nami. Also Chopper.. but I bitched about that already.
Point is, you're not crazy in noticing change. It is there in every aspect from the way they look to the way they act. This isn't bad; change is what keeps things alive.
If you want to argue the characters have changed in both the manga AND anime, that's a different story. Clearly there are differences after the time skip, but I've already gotten used to them. A few things that bugged me at first were Nami, Franky, and Chopper's new designs, but they work well once you get past the shock factor.
But to say they are completely different in the anime versus the manga is a completely different argument that does not work at all. Even with the fillers, which some are hit and miss as far as plot goes, I've never seen One Piece fillers do anything to make a character act out of character. Yes, they screwed up with a few PLOT points, which created plot holes for the anime canon, but that's also a different story. All in all, the characters are the same in the anime as in the manga. For argument's sake, the only characters I would be willing to discuss on this matter are characters like Hancock and Buggy that were used as filler generators during the war, which may give viewers a different interpretation, but even then I don't think they acted OUT of character, just hammed up their character traits far too much.