I'm not disagreeing about his up-b being a very important part of his kit, but there's absolutely nothing "burst" about it, it's a slow and committal move without much mixup until cancelled (frame 47 at the earliest). Again, it's a great move, and important for his mobility, but it ain't a burst option by any means and that's fine!
Nikita is crazy against off-stage opponents, sure, but it's no substitute for chasing characters playing keep-away on stage. Nikita is not a good neutral tool. Characters on-stage have a very easy time avoiding or blocking it, there are just too many options at their disposal for something as reactable as Nikita, and it certainly doesn't get Snake any closer to closing the gap if he needs to chase them down.
Relooking at his data on the cast rankings, bottom 3 was an overexaggeration, but not by that much. His mobility is truly awful, especially ground-to-air (say, for example, needing to deal with platform camping?). He has no drift, slow aerial acceleration, and a full hop lower than Doc. Dash attack is good burst but pretty unsafe on block. Otherwise his initial dash is nothing special and full dash is the same as Corrin/Ivysaur/Peach/Daisy. His mobility as a whole is bad, but...
...again, completely agreed that his mobility problems usually aren't a big deal for him. His zoning and boxing are both top class so it only really matters if he needs to chase someone down, which is rare -he has to have a stock deficit against a player who will actually commit to stalling him out, and even then it's not like that's just an easy win condition or anything.
Snake's a very very strong character, I completely agree in thinking that he is a very strong character with tools for basically any matchup. But I think it's a competitive disservice to just throw our hands up in the air and say "well he's busted I guess there's nothing to exploit against him." His approach options are pretty weak and he can't chase down platform camping effectively, so he's not completely flawless. Yes, that requires getting a notable lead in the first place, but it's better than nothing!