I really wish they would have just removed all the slowdown. The later NES Megaman games, starting with 3, are basically slide-shows at times.
The article linked leans towards the Megaman Collection as the "better" way to repackage old games, but I much prefer the approach Rare Replay took. I don't need 1:1 visual accuracy and all of the immense technical problems of older games like MM3 or Banjo Tooie. If I was that obsessed with playing the "first" version of the games, nothing but the real deal on the original console is going to satisfy.
Instead, I'd rather play those old titles with technical blemishes removed and a package that celebrates the spirit of the games, not an untouched museum.