I wouldn't say it's major or breaks the game, but it's noticeable. It's basically half-second jitters of the screen while things are moving. I don't think it affects my inputs or has gotten me killed or anything, but it's weird to look at. It's one of those things where I wouldn't be surprised if people don't notice it, and I could see myself adjusting to it, but it's definitely annoying.
I'm still enjoying the collection (played some challenges and am up to the Wily Stages in Mega Man 1) and it's still very playable. It's a nice package, and the extra 3ds features like the community challenges and the Japanese versions of the games are pretty neat (my playthrough of 1 right now is in the Japanese version, which as far as I can tell just affects the title screen, but cool nonetheless).
Edit for some additional notes:
There is 3D! But just for the optional borders you can turn on. It puts the borders in the background and the game into the forefront. Pretty weird use of the feature.
One or two of floor crawling enemies in the Fireman's stage seem to randomly disappear for no reason. I don't know for sure if that happened in the original version, but I'm inclined to think it didn't.