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I start to believe that it is a hardware timing issue with the cartridge (at least my copy which looks and feels super high quality btw). When power comes on the cartridge is still initializing/booting itself when the Mega Drive gives it control too soon. This explains why game genie in between works, because then the metal gear cart gets power and can initialize itself before it is given control to really boot.

The metal gear cartridge seems too slow on startup to be ready.
 

This does not work for me.  Also weird that it could work because the Sega does not hold state between power cycling!?
Only way i could get it to boot is to use a Game Genie in between. Which is kinda unacceptable as it makes it dependent of that Game Genie cart (if that stops working, you're stuck with a none booting Metal Gear game cart)

I do have a Suzo "The Arcade" which has two buttons which works on MSX. I did press that button yesterday if i'm not mistaken and did not do anything. So i guess it needs something special? A mod or? Which two button joystick do you use on your Amiga?
Does master system controller work on amiga by any chance? Or Amiga cd32 controller?
Answer my own question: Found this thread and seems master-system controller does work. With mega-drive there's discussion about safety). And perhaps 2600 controller could also work.

I'm not used to use joystick up to jump. Now i remember why i don't play platformers on Amiga ;-) I make mistake after mistake and this lovely game becomes unplayable for me. How do others play this game? I have a Suzo Arcade stick which has tight controls (micro switches).