I'm sorry but deep doesn't describe X6's level design. More like cheap, bullshit, and frustrating. Case in point; putting a lock on pass through wall projectile enemy in a zone where you need to remain crouched or the ceiling will magically crush you. But of course standing up, getting hit, and in some cases, attacking, will stand your ass up and cause you to be insta-killed. The mere fact that they even left in such a bullshit mechanic like that is bad enough, but that's just the beginning of the crap X6 spews from every angle.
X6 has some really bad level segments in some places. It was not thought out at all. It was a failure in level design, and in engaging difficulty. Their idea of difficulty was not particularly skill based, but rather luck of the draw or grind for power-ups till you can just survive the bullshit.
The parts system especially urked me. Getting parts was fine. Yeah OK they could die, that sucks, but it was a repeatable process, and quick to find a few right away. Too bad you cant equip them, until you grind the same damn enemy over and over and over again. Once you collect enough EXP- err nightmare souls, then you can finally equip one [tornado fang]ing part. That is bullshit.
Notice a pattern here? Grinding? Keep that bullshit out of my Megaman X games. So now lets look back. What was so great about X1? No grinding for parts, money, items, etc. It was straight up action, with a little exploration. You find stuff and can equip it right away. No waiting for all 4 parts, or having to grind money or 'souls' before you can even think about using the power-up you just found. It has proper game flow, which X6 can't begin to even think about.
The nightmare system seemed like a good idea on paper, but the next time you decide to randomize an item, or capsule, DONT. I spent nearly a half hour trying to get the capsule in dung beetle's stage.
X6 was almost a complete failure at living up to what makes a Megaman X game good, and in a lot of cases, what makes any game good. Anything it fixed, it turned right around and completely broke in another way.
Then of course, X7 took all these problems and just added more to them. Abysmal.