3 wins in my book, extremely closely followed by 5, on the merit that 3 might be one of the most interesting, memorable and challenging titles without resorting to endless spike mats or bottomless pits, with just enough mechanics between Rush and the sliding to be interesting and challenging in a new way, but without feeling stuffed with gimmicks and one-shot systems... but unfortunately it has a few very severe problem spots that hold it back a lot. To the point of almost being unforgivable. Almost.
So that lets 5 catch up, and that is, in my opinion, a nearly perfect game. Yes, it's quite easy, but since when is that a bad thing? It's a bright and cheerful game much like 2. It has consistently great music... Not the best of the series, but none of the series' worst tunes, either. I'll gladly hum along to any one of the robot master stage themes, and the Protoman's Castle theme is an underrated gem. And yeah, sure, Charge Man is a train and Stone Man is Hard Man but made out of stone, but I still feel like there's enough personality in there, and most importantly, it's just fun to play all the way through. I also enjoy what they did with the plot, as little of it as there is. Come to think of it, since Proto Man was a big deal in 3, didn't show up in 4, and was made the focus again in 5, I guess it makes sense that I feel like 5 is somehow the true sequel to 3... I'm left wondering if 5 gets consistently rated so low simply because of being such a late entry in the series, and specifically coming out after 4 wore everyone out...
4 and 6 tie for last place in the NES series in my list. 4 feels unusually nonsensical even for a Mega Man game (Toad Man? Pharaoh Man? RING MAN??? Oh yes, ring man, you know, the guy with the rainbows.) and in spite of that, it can't help but reuse gimmicks and boss powers from earlier games, more so than 5 or 6 do. On top of that, there's a very high concentration of insta-death rooms with pits and spikes, and those challenges just don't feel engaging to me. Meanwhile, 6 has arguably better design overall but I guess in an attempt to bring the difficulty curve back up after 5, everything just feels sluggish. Too many enemies take too long to kill, stages go on for longer than they probably should, and none of it just feels very interesting. Uninspired, I suppose. Possibly the blandest game in the series, in spite of solid ideas, gameplay and stage/boss design, so even when it plays well, it just doesn't feel very fun.
Don't ask me about 1 or 2. I can never make up my mind about those.