It's hard to tell, while playing the newly released Mega Man Legacy Collection for 3DS, whether the constant framerate drops are a new problem or an old problem. It's easy to look past them, though, because Mega Man. This collection, which is out today on 3DS and also came out on consoles and PC last year, includes the first six Mega Man games as well as a number of optional challenges. There are a couple of modern conveniences, like an options screen and a save file so you don't have to write down passcodes for each game, but otherwise these are faithful emulations of their NES counterparts, warts and all.
So when there are too many enemies on screen, the framerate will slow to a crawl. When you scroll between areas, the right edge of the screen will flicker. There's jank all over the place, just as there was on the NES. And Mega Man 4 is still the best, just like it was on the NES.
I've been playing this version of the game for the past few days, and I'm digging it a lot. If you're looking to revisit Capcom's nail-tough platformers, you could do way worse.