Right. The best is Xtreme2.
X6 remains my favorite main-series game, which is not to say I believe it to be objectively the best. I see many production value issues and yes the Nightmare System is more annoying than anything else. But the core level design outside of the Nightmare System is generally well done, especially since among the abundance of power-ups there is not a single one that requires a boss weapon as either X or Zero. It's one thing to hack, password, or New Game Plus your way into starting with everything. It's quite another to earn it yourself, conquering every nook and cranny of the stages without any boss abilities. X6 is the only game in which this is possible. The challenge level is engaging, although admittedly this is not the way to cater to a wide audience. But to the people who know MegaMan inside and out, navigating these levels requires every trick in the book. It's like the Lost Levels of MegaMan. At the same time no obstacle has only one way of clearing it, so it affords some level of personalized play style.
Perhaps X6's single best step was releasing the restraints of X5's convoluted power-up system and outright abandoning its ranking system (you're never punished for taking too long, taking too much damage, killing too many foes, failing to use a boss's weakness, or killing bosses too early). You can get everything, you can get it all with any character, and you can equip it all with any armor. As brutal as the game is, by the time you've cleared it all you are a [tornado fang]ing
TANK, and the best part is that the game's enemy mobs, Gate's Lab in particular, are so insane that even with all that power, combat is still engaging and you still can't afford to get too reckless. No other X-series game has that level of scale to its battles. X6 may not be for everyone, but if you're up to it, it is an experience like no other.
The Nightmare System is really what needs fine-tuning the most. At the very least seeing what effects are present needs to be more user-friendly, so that the Stage Select doesn't display only the most recent changes. Also even though Use Previous Data remedies this just fine on PS1, allowing Stage Exit at all times would help streamline things. And of course, the infamous Sentsuizan is the textbook definition of why the ability to turn a saber skill off isn't a bad idea.
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)