-I see what you mean with the weapon restrictions and how they conflict with EX skills being allowed.
-In regards to MMZ3, here's the summary. The body chips I mentioned earlier are attachments that you find via secret disks that give Zero special powers. They are divided into 3 types; foot, head, and body. Foot chips make your character more maneuverable, making combat more fluid. There's frog jump (jump when touching the surface of water), double jump (return of X4 ability), shadow dash (pass through people, mantis battle can be brutal without this one), some chip that prevents slipping on ice, and ultimate (all powers in one, *spoiler ahead* find Phantom in cyber space and defeat him to get this one). Head chips give powers such as quick charge, very slow regeneration if stationary, and one other one I don't remember. Asides from elements, body chips give powers such as not causing some floors to collapse and preventing Zero from being shoved when damaged. These are found by defeating bosses. Cyber elves have been broken up into 2 classes. Fusion elves act like the cyber elves from previous Zero games. Satelite elves give the player increased power without being used up. Most of these elves tend to have considerably less powerful effects than fusion elves. A lot of the new EX skills that don't require elements to use are pretty good (especially the sword and shield boomerang skills). It's a shame that most of the gun skills require elements, since one of them is one of the best skills in the game. The non element gun skill is still great though. (Better than the MMZ2 one.)
-In regards to Mega Man Legends, only the buster should be allowed and the combined levels of the four attributes should be no higher than 12. (I don't remember the level cap for each attribute though.) Sub tanks and armor (level limit of armor is up to you) should not be allowed.
-For the blind fighting challenge, players should only have to fight the boss while blind fighting (they can reach it normally). I don't know if special weapons should be allowed (classic and X only) for blind fighting or not, but if they were, exceptions should be made for the really broken ones (Thunder Beam, Metal Blade, Storm Tornado, etc).