"One of" his favorites, yes (MMXOCW, page 57).
Of course, that is another thing X6 could have specified better.
Perhaps, but Capcom's guilty of the same thing when it comes to explaining Sigma's demise. In both X5 and X8 they failed to do so properly. For that matter they also failed to kill Zero properly in X5. Boss explosion? Seriously? In general I'll take X-series over Zero-series any day, but Inticreates DEFINITELY one-upped them on that one.
X6 is my favorite main-series X game, no doubt. It fixed a great deal of what was wrong with X5 (parts system, ranking system, player-specific availability of power-ups, linear armor setup, Zero's moronic boss AI), and its core level design is among the deepest the series has seen. There's a slight touch of "Metroidvania" in it as nearly every stage forks and near every impass has multiple solutions, allowing greater leeway for individual play style. There's an insane level of power-ups to collect, and at the same time, an equally insane number of enemy mobs to plow through, providing a greater sense of scope to the fight through each stage than any other MegaMan game. You're powerful enough to take on gigantic masses without having to tip-toe through them, but at the same time can't afford to get too careless, an excellent balance.
At the same time, I can see why the game isn't a crowd-pleaser. The enemies and levels provide a far more head-scratching experience than MegaMan is known for, and the series in general is already considered difficult by non-fans. When players are greeted by shoddy localization and some admittedly low-grade boss sprite work, it's easier for them to simply dismiss the game as broken and give up. The Nightmare System is more often than not an annoyance, particularly in regards to the complete inability to return a stage to its neutral state.
I often refer to X6 as being to Mega Man what the Lost Levels are to Mario. They reek of low development time, they're tough as nails, they're exceptionally rewarding for those players who are up to the challenge, but they're also not the best way to win over new or less dedicated fans.
I love X6 to death, and I maintain that the majority of players who complain about its allegedly "impossible" segments simply gave up too easily. I have completely lost count of the number of times I've had to correct people on what the bare minimum requirements are for any given obstacle. I can see why its not a very approachable game, but at the same time, I'm glad that Capcom threw the (for lack of a better term) "hardcore" fans a bone, because it was freaking awesome.