Mega Man 6 is an odd one. The Rush armors introduced some major changes to the gameplay, and the stage design is all over the place.
Blizzard Man, Plant Man, and Centaur Man are the best efforts it puts forth in the main stages, and they're all decent in the context of the series. The others have a handful of good ideas spread too thinly, and the split paths cause the same problems I praised Mega Man 5 for avoiding, like having one "correct" path that leaves the other to be ignored forever in replays. The best we got from that was an optional mini-boss, but dividing the content between two paths made those stages some of the weakest thus far.
There was a decent collection of small enemies, and most of these were used well, but there weren't enough that could cause the player any serious trouble; certainly nothing like an Apache Joe. The best moments made good use of the smaller enemies, but there was a lack of big, impressive traps or fights that often define a stage, and the Robot Masters are equally disappointing overall.
The armors save it from mediocrity, offering ways to explore and engage enemies that weren't possible before. This is problematic, as the player can easily complete most of the stages before discovering them at all. While Rush rewards from bosses used to be an unnecessary bonus until the Wily stages, they are now the source of most of the game's fun.
The end stages relied too heavily on reusing similar groups of enemies, but their stage design and bosses make an extra effort to give the player lots of unique things to do with the armors. Getting this part right is the best quality the game has, even at the cost of making the weapons and Beat mostly useless at the end in comparison.
Overall, Mega Man 6 has some of the worst main stages of the original series and not enough high points to make up for it, but challenging or creative design isn't everything. The new play styles made possible by the armors add a great deal of potential enjoyment to the most basic of enemy encounters, and the opportunities for players to put them to good use in the latter half are surprisingly well thought out.
When treated as a playground for Jet and Power Mega Man, the game does okay for itself. For some this wasn't enough, and it's entirely fair to put this in the running for worst NES Mega Man game. Personally, I found the changes to the formula fun enough to give this just as many replays over the years as Mega Man 4 and 5.