BTW the Retroarch genesis plus gx core can eliminate the slowdown completely of this game with its overclock option, it is even playable on Android phones using Retroarch. All we need now is a hack to switch between special weapons with the trigger buttons without having to open the menu.
I'm not sure if y'all are familiar, but since the game was originally released in Europe/Japan it's set for 50hz televisions. Patching the game region to US changes the frequency to 60hz and speeds up the game. There's also a cheat code you can use to get more bullets on screen, and to walk without pausing. The patch hosted on this site also allows SRAM saving, rather than EEPROM which causes errors, allowing you to play the final Wily Tower after beating all 3 games. If any of you have downloaded the multirom set for ps2 soft-hack that lets you play snes, nes, and sega games on the PS2 the Pgen emulator doesn't shade the bosses you have defeated in the Boss Select screen so it's harder to keep track of your progress.
As for switching through the weapons one problem with this is that on the original Sega Genesis controller there is no select button, L or R triggers, and only 3 buttons (A,B,C) on the controller. Also, I was briefly working on this and it looks like the Pause menu is necessary for loading some important function in the background. I was able to hack the RAM to change Megaman's suit (that corresponded to the weapon upgrade) and this immediately changed the suit on-screen, but when doing the same for his weapon it would not upgrade his weapon on-screen. Even after hacking the RAM to give him appropriate weapons you still need to pause the game for it to change the graphics, store all the crap in VRAM, and apply the new specs for the weapon.