OK, just tried the game out. Here are my gripes.
Bullets are too small. In the arcade you know when you're about to be hit, but with this you can be hit with a little 4 pixel blue ball without knowing it.
People come back after you kill them. So damn annoying, I kill a whole bunch of soldiers, go forward again, realised I've just missed a weapon, go back, and there they all are wating for me again... not Metal Slug style at all.
The weapons disappear too fast. You have about a 2 second window of opportunity to pick up a weapon otherwise you're out of luck. This combined with the serious lack of weapons in the game severely annoys me.
This one isn't major but the animations are slightly choppy - perhaps they had to make it that way to fix their slowdown problems?
The autofire makes the game way too easy, they should not have included this feature at all. Even pressing a button the fastest you can won't get it to fire as fast as with autofire on. I played the game twice through - once without autofire, and once with, and I can tell you that with autofire it was a piece of cake.
My last annoyance is that overall it just feels like one of those 'normal' platform games. The people respawning after you kill them, the 'life' system (although I guess they had not much choice when porting it to handheld), and the jump around bits, where if you fell down you had to go back and around again (and face all the enemies you've already killed). IMO it would be better if you just died when falling down, although this wouldn't work well with the life system.
Despite all these flaws I do actually believe it is a great handheld game and I do actually enjoy it (hard to believe I know).