Yeah, I definitely agree. I mean, you're pretty much doing the same thing for every mission; 4-5 and Ex9 are the only real exceptions and the closest thing to a survival mode the game offers. It would have been cool to have true variety with the missions, and they should have done that. It wouldn't have been that much more difficult to mix things up using the same assets and mechanics and also offer a true, endless-survival mode.
Capcom are smart, though. They knew they could get away with the bare minimum because of how slim the pickings are right now. This time next year, folks will likely be laughing about how paltry Mercs 3D is or completely forget about the game altogether. It's admittedly addictive fun but should have been more at $40 (what I and a lot of other folks paid for the game).