An option to split the squad on-site and have some people wait while others go infiltrate or whatever would be very good.
Also, it would be useful to have interface show the current stealthiness or disguise efficiency for the squad or part of it.
I also have an idea for a rather more sophisticated combat improvement. Every character could be either 'in cover' or 'in open'. People in cover would be vastly harder to hit than those in open, going with the assumption that in a real firefight it's indeed cover that keeps you alive. Dodge would be much less effective in cover and thus be a skill for people who, for some reason, find themselves in open.
Characters would go into cover automatically when combat begins. However, if they'd not expect to be attacked(like NPC's who don't see weapons on the players), they'd only have a small chance to find cover in time before the shooting starts.
Attacking in melee would automatically put you in open, but melee attacks would also ignore cover. Thus melee fighters going against shooters would need to kill them all in one turn or be in big trouble, unless they're also dodge monsters. On other hand, really good melee fighters would this way be able to kill weak opponents faster. You'd also have the option to 'rush out' with a firearm - losing cover for the next turn but also denying cover to the enemy you're rushing out(unless they got great dodge, then they have a chance to foil you!)
Finally, the game would keep track on how much noise(shots) you make on a site after the alarm has been raised. The more shots you fired overall and the more shots you fired recently would contribute to the chance of enemies encountered starting in cover or, in rare situations, even getting a first shot. This would be counteracted by stealth.
I imagine shooting against proper enemies being in cover would be a much more drawn-out affair than normal, which in turn would mean you're alerting everyone else, giving police time to respond and using up ammo. On other hand, rushing out out of cover would be very risky unless you are confident the final attack will disable all enemies. You could make drawn-out fights in some situations actually automatically attract extra enemies, automatically starting in cover(or even getting a free shot), making finishing the fight fast even more important.