Actually, I prefer SM64 on a certain level too. IMO, SMG1 & 2 have overall superior platforming, but the games feel less cohesive and more tedious than SM64.
My biggest gripe is probably the overall level design. Yes, there are some very creative levels in SMG, but they are very linear. In Mario 64 there were a lot more "open world" type levels. When you entered a world you were given a hint like you are in SMG, but in many cases you could actually collect any star in that level. If you happened across another star while going after the hint star you could collect it. In SMG this is largely untrue because the levels are altered, often dramatically, to funnel you to the hinted star. There are exceptions (e.g. some hidden stars), but overall this is true.
Also, and maybe related, I'm not a huge fan of these levels with random chunks of the level floating everywhere. Maybe the linearity and these random floating chunks of land is what gives them more flexibility in the level design, but the levels just don't feel much like actual worlds... if that makes sense? Every level, and thus the entire game, sort of feels like a hodgepodge of arena-like challenges rather than cohesive worlds. Sort of like if SM64 had had some DLC challenge levels you might end up with crazy nonsense like in the SMG games.
I also HATE the star bits. Hate them. Collecting that crap is tedious and doesn't fit the game at all IMO. Not only do I hate collecting them, why can I, the user, shoot star bits out of the sky like I'm the hand of God? I know Mario games are crazy and pretty much make no sense at all, but this really bugs me for some reason. It really creates a clear separation between Mario the on-screen character and me as the player. I'm sure most people won't care, but it bugs me.
I also hated the hub world in SMG1. There was something somewhat fascinating about getting to explore the castle in SM64, but that didn't apply to SMG1. SMG1's hub was boring, tedious, and just flat out annoying. Thankfully, Starship Mario and the map access to levels fixes that problem in SMG2.
Those are my main complaints about the SMG games. The camera can become less than ideal at times, but that's a problem they've all had since going 3D... including SM64. Overall I really am enjoying SMG2, much more so than even SMG1, but I still long for the SM64 at times. Because as noted above, sometimes SMG just doesn't feel like a true SM quest... it just feels like a random collection of crazy platforming challenges with wildly fluctuating difficulty to boot.