I remember when Gen 6 came around, and as underwhelming as it was visually, those games had notable framerate drops that I just found embarrassing. Sonic has consistently hit 60fps in more mainline games than Pokemon has. But after that, the Sonic series is a series that is consistently inconsistent. It may run smoothly but you'll run into some other problem.
If we can say Pokemon is like a car stuck in the road, just running tires in the mud and moving slowly, Sonic is a car where the suspension gives out at every other turn, and crashing into something shortly thereafter. You're getting somewhere at a much faster clip, but that doesn't mean the ride is well. One is part of the largest media franchise on earth and the other is a series that they don't even try to argue for a full priced release, so these are things to consider when considering their struggles. One can get the financial backing to address that if those involved really pushed for it, which makes the struggles infuriating. Like Castlevania in 3D, another iteration of a 2D series that gets dogpiled on, all of the issues people have with these games go right back to cost, and Pokemon increasingly has little excuse to get away with what it does besides it not costing them money to not step it up just yet.
Sonic Team has also made non-Sonic Games, and if we even consider those for a moment, Game Freak is clearly a company that struggles despite the major IP it has behind it. People picking Sonic Team better be doing so because they're thinking of just Sonic the Hedgehog. I can't even imagine Game Freak doing a game like Phantasy Star Online well, at all.