Again, I am reviving this thread, this time to say that I am really burned out on this game. I started trying to improve my run again but after three stages I started to get a feeling this run would never be finished. I would still like to see a new Mega Man 6 run and I want to encourage anyone who has the time and energy to try their hand at this game. I would be more than happy to help in any way I could if someone picked this up. Now I'm going to list some of the things that should be done better in the next version.
The biggest errors in my old run are in the boss fights. The bosses in MM6 like to jump a lot, and it's not always easy to manipulate them into keeping their feet on the ground. I lose a lot of time because of bad luck manipulation especially the second time the bosses are fought.
Overall precision. The old run was done with Famtasia, which means that menu handling, jumping, shooting and sliding can all be done a lot more precisely.
Some of my decisions were just BAD. For example the end of the Plantman stage was horrible. You can see the changes I made to it from the FCM below.
There is also something I never tested: the shortcut at the beginning of Yamatoman stage. There is a destructable block in the second or third (or was it the first?) screen in the lower right corner. I always just assumed it was slower because it requires you to change into the power adapter for a considerably long period of time AND fight a miniboss, even though the distance you have to travel is shorter.
I also never tested the long route in Dr. X stage 1 (the space-themed stage).
I'm in a hurry right now so I don't have time to think if there was something else, but I'll edit this later if something comes to mind. You can find the video of the first three stages
here. Note that the strategy used in the Flameman stage is apparently SLOWER than the one used in the previous version, so scratch that.