Adding seats to the vehicle by sacrificing your equipment? I like!

There's not really a need for separate equipment slots on vehicles. Infantry only need an equipment slot because none of their normal gear is active. All of that stuff could just be normal active mods on a vehicle.

It's different from EVE ammo. Secondary weapon systems will be, as their name suggests, secondary. For example, here's another idea that came to mind: light auxiliary blaster (HAV only for now). You switch from your main turret to the LAB. It has decreased damage output, which is why it's secondary. But it will be limited on ammo, but will have a fair amount as opposed to a guided missile (for example, 100 rounds for the LAB but 2 guided missiles).

The only usefulness for the LAB will really be useful for pairings with railguns and missiles. It will be better for taking care of infantry than a railgun or missile, depending on situation. It gives railgun/missile HAVs the tactical advantage of being able to deal with infantry themselves, but it will be inferior to its 'parent' system (LAB will have less damage output than even small blasters, but I'm thinking it could have high damage, low ROF, such as an auxiliary HMG on a tank in BF3).

General characteristic features of secondary weapon systems: limited on ammo, goes into a vehicle equipment slot, and has a 'parent' system but the 'parent' system will always be superior (guided missiles can have high damage outputs, but long reload times and extremely limited on ammo such that its parent system, missile turrets, are superior). You might be able to switch back from a secondary weapon system while it's reloading though, or will have to wait until it finishes reloading the next round or clip, depending on balance.

Long post hehe. Got excited