FYI: In any "special weapon/item required" Classic scenario, it is unlikely but still possible to get stuck by simply running out of energy. It's something I've heard brought against MM3 in particular with its Rush segments/jumps.
Also, I agree with Flame on the whole "default air-dash trivializes the leg armor" thing. I mean, I realize that X looks kinda gimped when Zero and Axl default with it. But the alternative is that the leg armor's value is severely diminished, as whatever additional gimmick it offers probably won't compare to Zero's double jump or Axl's hover, making it a poor choice for a stand-alone upgrade.
I like X6 for what it did... It's still flawed though. You bring up Metroid in your argument, but the design philosophy in those games is not the same thing. You can't get into an area in the first place if you're missing the necessary equipment in the first place in Metroid (for the most part).
What exactly stops you from entering Turian with the Wave Beam? Hell, what INDICATES IN ANY WAY WHATSOEVER that you're supposed to forsake it? In nearly any other area in the game, the Ice Beam is the pits.
The thing about NES games is that they were EXPECTED to screw you over through lack of information. It's just what they did. You know, 'cuz back then we felt special for buying magazines that explained it to us. Obviously that doesn't work for the modern 50 hour adventure. But a traditional X-series game, no matter how pretty its graphics, is short enough and contains enough checkpoints that I feel the occasional hiccup can be forgiven. Especially if the odds of running into a serious problem aren't all that great to begin with, and the likelihood of X6's "traps" actually catching you off guard is greatly exaggerated. See below.
Such is not the case in X6. In X6, you can get into areas you are completely unable to traverse, and guess what? You can't backtrack out like you can in Metroid, effectively leading you to restart the area completely.
Again, Gate's Lab 1 is the beginning of the stage, before any enemy appears, so no progress is realistically lost.
Gate's Lab 2 applies to two out of five (six if UA code is active) player/armor choices, and that's assuming you have none of the above-mentioned weapon/part solutions handy. Being well into the late-game, this is less likely. The only way it realistically catches you off-guard is false confidence if you're replaying after first clearing the level as Zero (since the trouble spot is X-exclusive). Unarmored X exists solely for bragging rights; you should NEVER be using him on your first playthrough. Shadow Armor requires clearing equally difficult jumps just to obtain its parts, so the value of Hyper Dash to one who has no air-dash or Ice Burst has already been taught within the game.
Speaking of tough jumps required to get a Shadow Armor part, Metal Shark Player's alternate route is clearly meant to be accessed with Hyper Dash (or Nova Strike), which in turn gets you across the pit. While it is POSSIBLE to access the alternate route without it, this requires not only careful timing but also decent knowledge of the game engine in terms of milking your dashes and jumps for maximum speed. In which case, use Wolfang's weapon for the pit.
Frankly, I'm amazed more people don't complain about Commander Yammark's alternate route. I mean, it's still an alternate, but it truly is the worst obstacle in the game. It's in a Nightmare effect area with HIGHLY disruptive effects (either the search lights or the rain can screw you), and with an access route that invites the Shadow Armor (dashing from the ceiling to reach the high route in the main stage). The only good news is that there's nothing beyond the pit other than the alt boss door, so if you do suicide your way out, then the only thing you missed is a few extra Nightmare Souls from Dynamo. Then again, for a first-timer, that can be discouraging when you make the return trip just to find that out.
If they had more time to work with, X6 would probably have had those kinks worked out and it would have been even better. But yeah... hindsight is 20/20 right? Fact of the matter is they didn't have much time, and here we are with a game that had high aspirations but fell flat a bit in the design phase. Such is the way things are with time constraints.
Unfortunately it's not always development time that causes that. We waited quite a bit for X5, and I could make the same poor-implementation arguments there. Actually, far worse so, in that while you can plan around X6's "flaws", there's a lot wrong with X5's level design that you simply cannot work around. ESPECIALLY the implementation of the Gaia Armor. It's virtually impossible to obtain without having visited all 8 Maverick stages already (and using "mad Zero skillz" alternative requires forsaking the Speedster for Jumper, something you should NEVER do in any X-centric playthrough because it cripples the Falcon Armor). This means that the first "new" stage you get to use it in, Zero Virus 1, is the very worst level in the entire game to be using it.
Do note I do like X6 more than X5. I just wish I could run through it with nothing like I do in any other X game that lets me. To this day, X2 is still my favourite for that sort of run (and tied with X1 for overall).
Honestly, while I'm not generally an "unarmored run" kind of guy, I like it best in X3. Mainly because I hate X3's buster so much... Also, charging a close-range Z-Saber in half the time isn't without its benefits.