Make it so there is a 3rd skill slot for 'gun skills'.
These would all be skills that only effect your gun.
Some examples:
Frost Ammo- your shots slow the target by 35% if hit (Bombz idea)
Double Bullet - your gun shoots 2 bullets at once for more power but faster ammo use
Better Reload - your gun reloads more ammo then normal from each reload picked up
Charge Up - you can hold your shot for a few seconds as it 'powers up' and then when you release it, the bullet will do much more damage. If you don't charge up its just like normal.
Static Shock - your bullets have a chance to damage other nearby targets if it hits a target in a crowd (the other targets would not fall down though).
Full Auto - you can hold down the shoot buttons and your gun will continuously fire
some guns would not be compatible with certain skills though. my idea is to classify each gun as a different 'class' (A, B , C, etc) and each skills will show which classes its compatible with when you hover over it. for example triple beam couldn't use double bullet.
EDIT: other idea - make it so u have to sacrifice your passive skill to use a gun skill
thoughts?