I mostly agree with you, except that I truly think X6 is designed poorly, and it's partly from whence arises the absurdly addictive difficulty that's managed to attract a cult following. It is truly the "Lost Levels" of Mega Man X, and that's one of the few arguably positive distinctions I can bring myself to acknowledge about it. As for why it's designed badly, I'll give a few examples, but before I do, I'll note that while the Nightmare System is ultimately one of the biggest reason people hate this game, it had potential to be something much better and much less stupid. It was a decent idea on paper. No reason it couldn't have succeeded at least as well as the similar mechanic in X1, so I won't focus on it right now. Here are my problems with four of the stages, for starters, (assuming I'm playing as either armored X or Zero) along with any good things I have to say about them:
[spoiler]Rainy Turtloid: Too linear and repetitive. Reminds me of X3, but much worse. Also, those spiked corridors you need pinpoint accuracy to get across? That's cheap, and a waste of my time. There's really no fun I get from learning that elite skill, and the payoff just isn't worth it. Rainy Turtloid seems to be channeling Aqua Man by way of Astro Man judging by his signature Meteor Rain attack, and he sure likes to stand around and give me ample time to ruin the gems on his back. *Shrugs* I guess he's all right, but I haven't got much else to say about him.
Blaze Heatnix: The miniboss. The rest of the stage has hope, I'll definitely give it that, but spamming the miniboss just wasted any possible fun that stage could've had. This was truly a stage that suffered the crime of rush development. As for Heatnix, the worst I can say about him is his name. Why didn't they just call him "Blaze Phoenix"? Making the surname of these Maverick's some stupid mashed-up non-word just makes them sound dumb. The fight's not bad
Metal Shark Player: I actually sorta enjoyed this stage except for it's slight case of cheap enemy placement. First case happens near the end of the first crusher where you have to duck in the ditch in order to not die. Once you're ducked and the compactor is down, letting go the down button shouldn't kill you, but whatever; once you're ducked, this Nightmare [dark hold] comes from the end of the screen and 9/10 will hit you, forcing you to stand up and meet instant death. Have fun repeating that segment 2 or 3 times. Then there's the other segment at the end of the next crusher segment, where you have a long stretch of instant death zone with a Nightmare at the end of it. Also that block puzzle at the end can [tornado fang] off. It's boring. Metal Shark Player, on the other hand, is not boring. Just slightly plagiaristic. I know it's supposed to be a cool nod to classic bosses, but when it comes to new games, I really don't care much for recycled content. That's part of the reason why I don't remember much of the Xtreme games and part of the reason why I think X5 is terrible.
Shield Sheldon: Shortest level of all time! Wow. Unless you take the secret level path, which you can't know beforehand, so if you accidentally go into the iconic boss corridor first, you can't turn back. Lovely. Also those lasers in the secret path are just another game of stop and go, but with less of the urgency of Metal Shark's stage and the annoyance of those stupid Nightmare bugs. The false wall was a nice touch though. Sheldon will also be getting off easy, since I don't really consider him a bad boss at all. Just a badly named one.
Infinity Mijinion: Cool music, cool giant robot, and even cool flying ships that almost convince me I'm playing a sidescrolling shooter. I think I would've actually enjoyed this stage, though, had it not been for the Nightmares (but then I'll safely say the same thing about every single stage of this game). Other than that, it still suffers from repetitive level design. From start to finish. Infinity Mijinion suffers from the same problem, but he's been cleverly designed to manipulate that flaw into a diabolical strength: layering himself upon himself at random. This causes him to be about as wildly exhilarating a challenge as the rest of his stage, but it's less a challenge I can learn to love and more one that just requires desperation and getting it over with quickly. It's hard, but that doesn't make it great.
Blizzard Wolfang: Pretty good use of secret areas and a slippery upslope, but a fast enough player can just bypass the avalanches and witness their stationary spawning point several times. That being said, not a bad obstacle. This stage only suffers from a single case of repetition--the ice block pits--but placing a spike pit in the very center of the second pit was just cheap. No way you could see that in time to avoid it once you take the plunge, and I'd consider it pretty basic player instinct to figure that the center of the floor is safest while the edges are booby-trapped. That's all moot, though, if I actually could've seen the spike pit for a little more than a split second. Wolfang's not a bad fight. He's got a fair amount of tricks up his sleeve.
Ground Scaravich: A stage that changes every time you play it? Sure! That's pretty cool. If it weren't for that one stage module that doesn't allow you to progress without an air dash or a jump upgrade/hyperdash chip, or the copious amount of Nightmares and overly blocky design, it might be my favorite stage of the game. Oh, but that screeching soundtrack has got to go. The fight with Ground Scaravich displays the best use of zip lines yet, although that doesn't endear me much to them.
Commander Yammark: It's a nice stage, but kinda dim and boring. Those slow snail pads kill the flow one you get to the otherwise impassable spike labyrinth, followed by the dickish leap-of-faith segment right after it, and then comes the big [tornado fang] off gauntlet of giant Mantises with homing sickles. Challenging, I guess, but why not just have them die after the first explosion? There's enough of them to catch you off-guard with off-screen homing sickles without them coming back. Why are they immortal? What makes them so special that not even the Nightmares can match their malevolent unwillingness to obey the laws of nature? Not even Sigma regenerates that fast. He needs help.[/spoiler]
The best compliment I can give to X6 is that it probably had the most interesting boss fight ever concocted: Gate. What a brilliant fight. You can't damage him just by shooting him. You have to use his weapons against him. It's a truly sublime variation on the theme of acquiring and using boss weapons, but more than that, the fight is all about strategy. You can't bull-rush him. You have to be meticulous, and you have to make him go where you want, not the other way around. Unfortunately, I believe the game that is X6 failed Gate, Nightmare System and everything.
Is X6 better than X5? Well, it's definitely more special and memorable than X5, and where X5 fell short, it did improve. However, I might go so far as to say the stages in X5 were better designed. Yeah, the parts system sucked, the whole catastrophe mechanic with the Eurasia thing sucked (but like the NS, that also had potential to be good), the ending was dumb, and I personally think rehashing the X2 fight and ripping off Gamma at the end sucked save for the fancy new tune from the former, but overall it felt more playable. Albeit by a small margin, because the armors also don't deliver that well. Even though the Gaia Armor is like if X went to Tony Stark and asked to borrow his Hulkbuster, he's just too slow. I do like it better than the Shadow Armor, but that's me. I can see how the Shadow Armor succeeds where the Gaia Armor fails, but then the Shadow Armor has the piddly little energy shurikens where the big G has projectile-annihilating shots you can fire in quick succession. Now that's pretty satisfying.