These tips are arranged in chronological order. But before I go into the tips I want to say that you did an awesome job on this speed run. I honestly couldnt have done a better job. Mad props brotha!
And now the tips:
For the First Level, Nightcrawler can get the job done faster instead of wolverine. Although, Wolverine does make it more entertaining only because of the fact that everyone loves wolverine. You probably chose wolverine because of the 3 ice walls you have to break. The first one, you can break very quickly (2 air kicks, first one can be executed so fast, that it wont even show it on the screen), the 2nd ice wall, you skip it completely, go under the platform, and jump on the next platform. At the end of the level, right before you kill the 2nd to the last ninja, prepare to warp, kill the ninja, and warp onto the wall and finish it off with a mid-air kick.
2nd Level Part 1: Those things that you bust to open the doors, im just going to call them 'terminals'. The 4th and the very last terminal in the level, you can actually bust them through the floor with a mid-air kick (jump, hold up arrow, and kick {the move where he does a backflip and kicks up}). Doing this would be alot faster.
2nd Level, Part 2: 3rd and 4th terminals that are divided by a wall, use the floor trick I described above, accept hit them in this order: The one closest to you, hit it first, as you come down and go back up, hit AND DESTROY the one furthest away from you, then finish off the initial one with 2 kicks.
Pyramid Level (The level with the boss that throws rocks): It is possible to skip level with nightcrawler. But if said and done, I still dont know if you would gain any time due to the fact that the main boss will require alot of hits with nightcrawler (I could be wrong). And I have actually skipped a full floor before, so it is possible but very hard.
apocalypse (Spelling?) Level: I understand that you hit those brown balls on purpose for entertainment purposes. Thats fine as long as you have ATLEAST one yellow bar on your health meter when apocalypse shows his face. Becauase when you have a yellow bar, your super-move is alot stronger. You killed him in 36 hits, when you could have killed him in 11 or 12 hits (I dont know the exact number).
After the woods level, The level with the acidy looking water raising, so you have to climb at a certain rate so the acid doesnt own you (the level color is blue). -- At the end, right after you first teleport to get on the green flat platform, there is another platform where theres an enemy to the left, and another platform to the right. It would be faster to go left, get on the toxic waste thing, and teleport up 1 level as opposed to going right and teleporting.
The Transformer boss: You can probably beat him faster with Beast than Wolverine, although I don't know if you gain any time due to the fact that you have to switch all the way back to wolverine the next level, which would consume some time (again.. I could infact be wrong).
This last tip is just a general tip. On nightcrawler, I saw only once in the video where you did a diagonal kick on someone, and followed it up with a flip. I think this move can come in handy in alot of the game, but in particular the 3rd to the last level.
If your not familiar with it, the move works like this. If you flip, before you diagonal kick, then you cant do it. If you do a diagonal kick, and then a flip, the flip cannot be executed again, but any other move can be. (you basically cant flip twice in 1 jump and thats really the main law of physics on that move).
Any Questions about any of these tips feel free to ask.