MARINES
This is all about what your character is like. All marines would have their basic training, and proficiency in the standard weaponry. So training modules would be great for the marines who want to specialise in other weapons. This would obviously be linked to their overall performance, for example, "That was a lot of ammunition you burned through marine! I'll book you into a light machine gun course." This could lead training on the pros and cons of LMGs and tips and tricks.
'Marine sizes'
Now, customising your weapons and armour is fine, but what about different sizes of marine? A light scrawny guy can crawl through a venitlation shaft that the support machine gunner can't. Also, a little guy is a smaller target. However, the big guy can handle far more armour and won't get knocked over by the recoil from his oversized gun. Interestingly, a big guy who's a sniper would be able to handle the recoil of a larger caliber weapon than a small guy. But he'd make more noise as he snuck into a good nest before his squad attacks. A lean, lightly armoured marine could probably run further than his 200kg counterpart too.
'Perks and levels - Weapons'
A quick summing up of general thoughts I've seen on levels and perks advancement:
*Make them performance based, make them something that we can loose.
*Nobody wants to work hard shooting every enemy in the left eye so they can get some awesome accuracy perks, and just loose it all because of a bad day.
My take on those two ideas is one word: Compromise.
I reckon those perks should come easily with the lower levels, and be almost impossible to loose, but the really really awesome perks.... well, they shouldn't be something that you can achieve by playing for hours and not improving at all. How about faster reloads if you never fully empty your magazines and still just drop them? How about going for fast reloads, recoil reduction and a huge spread with a shotgun if you suck at aiming. Maybe you could use SMGs heaps and just 'spray and pray' until you get to use Light Machine Guns (LMG), then work on getting a minigun.
'Perks and levels - Loosing them (Oh no!)'
Yes, I do think you should loose the high levels of these perks. The highest levels should be heavily performance based. If you are at the top of your game and you can take the punishment from the stock of your auto-shotgun without loosing accuracy, then you suddenly change your midn and only use a silenced pistol with sub-sonic rounds for ages, your shoulder will get tender real quick when you go back to your shotgun. Perks should be hard to loose and easy to re-gain, but when you stop going to the gym, you start to loose the tone and muscle bulk you gained. If you change to only firing wildly from the hip, you're going to loose some of the precision you gained by lining up every shot.
You shouldn't loose a perk because of a bad day. You should loose it if you don't use it... or at least try to use it.
'Perks and levels - Other'
Now, what about other kinds of perks? Carrying capacity? Sprinting endurance? First Aid? Picking locks(or hacking electronic doors)? Armour weight? Stealth?
The more often you patch up a mate so he can limp back to your dropship with you, the better you are at it. The more often you carry too much to run for long, the better you get with it. The more you wear your 'running boots' and run around, the better you get at it. The more often you sneak around, maybe there'd be a key or combination to walk quietly, the better you are at it.
'Medics, do we need them?' or 'Training and it's effects'
Do we really need dedicated medics? How about having a limited number of courses you can do when you begin as a marine? So you start off learning say, pistols, SMGs, shotguns and assault rifles, basic first aid, basic armour repairs, grenades, and regular armour. If you're accurate, and you want to, you can do a course in sniper rifles. If you want to be a support gunner, you can do a LMG course. If you want to help your friends, you can do your advanced first aid. If you want to fix stuff, you can do a technician's course in a number of different diciplines (hacking, armour repair, remote piloting, etc). If you just love blowing things up, you could do demolitions (this would cover cutting holes in doors, as well as just blowing stuff up).
Of course, you could only choose two of those straight after basic. But if you show a profficiency to anything (you help mates, you shoot accurately, you 'spray and pray', you fix folks stuff, you use grenades well, you start to modify your armour) then you'd be offered the advanced training course that allows you to do more in that field.
This could be fun for the developers, as they could gradually create and release extra training where they feel inspired.
'Teamwork'
I haven't played all that many co-op games, but one idea I had was instead of just having stats on people, having an in-game, virtual dossier on your teammates before a mission to begin to establish your squad tactics.
Conclusion
Suggestions were asked for. I summarized my favourite ideas and suggested most of mine. I love where IM is going and I can't wait to find a new job and become a spearhead!
I hope my ramblings are helpful to someone.
I still believe.