A short list of updates that would add a lot more balance to the game and prevent exploitation of game mechanics currently not being used as intended by the developers upon launch (At least presumably, though that statement is an assumption):

Virus Upload Points
Exploit prevented, waiting for the oponents virus upload to complete so that you gain some sort of reward for retaking the objective since currently absolutely no reward is given to players who risk being ambushed trying to prevent the loss of an objective due to virus upload.
Method of prevention, simply give players 50 points for preventing upload, as much as a kill which is fair, and yet not as much as capturing an objective which makes sense, but is still worth it since you don't have to protect your upload while enemies are spawning.

Reactive Armor Module
Exploit prevented, using the dropship as a giant 'wack-a-mole' mallet and tanks as high speed people rams, instead of their turrets and weapons systems, as the primary method of attack.
Method of prevention, create a module that while not preventing the vehicles from crushing or roadkilling you, explodes upon impact dealing very high vehicle damage (Militia 1500, Standard 2000, Advanced 4000, Prototype 6000-8000). This module would have only a 1m range and thus only effect the vehicle impacting the soldier, and although most suits probably wouldn't equip it eventually, it would be enough of a deterrence to not have to nerf dropships or tanks unnecessarily and still make them behave the way they were originally intended to.

Area Spawning
Exploit prevented, going to the spawn sitting down and placing your radical right when the opponents head will spawn and unloading as soon as they spawn resulting in an instant kill with many prototype guns.
Method of prevention, making spawners spawn in an 'approximate area' instead of at a specific location, this allows players with the skill to push their opponents back to a spawn to still know roughly where the enemy will spawn and capture points accordingly, but not use this knowledge exploitatively. Additionally, to counter reactive spawning, all attempts to start your spawn counter at a location once virus upload has begun should be prevented, thus people already starting to spawn at a location before the upload began can still attempt to counter capture, but the team can't rush to spawn on the location, or have their spawn denied by virtue of 'not making it in time'.

Unlimited Swarm Launcher Lock Range
Exploit prevented, rushing out of visual range of AT suits, or hiding at high altitude and raining down fire, or on top of towers where the only reason the dropships are actually safe it by virtue of the fact that the game has a clipping range, but they are still capable of hitting enemies because actual projectiles do not have a range limitation.
Method of prevention, simply remove the limit of Swarm Launcher locks, they are already nerfed, this wouldn't make them OP, it would merely make them effective at their job and force dropships to take more evasive strategies or have their passengers do proper counters. Might also be nice to have a flare module created for dropships to direct Swarms off of them, and possibly as an additional bonus, increase the speed of swarm missiles, but give them a limited range after which they stop thrusting and fall to the ground, same with regular missiles (Though make both ranges significantly long).

Bonus Request =):

Remote Hack
No exploit prevented here, camping and using booby traps such as remote explosives on terminals is an intended part of the game I'm sure, HOWEVER, everything should have a counter, and this is my suggestion for a counter to that strategy.
Method of prevention, create a module with significant enough requirements that only a logistic suit could equip it viably (Normally although I'm sure some other prototype suits could field it), and this module adds an effective range of 10-20 meters from which a Mercenary can target a terminal he or she wishes to hack, and hack it remotely at a slightly reduced speed.

Spawns:
Already confirmed as a glitch that will be rectified in a future build. No need to keep going on about it.

Draw distance/vision range (the main reason Swarm Launcher range is limited):
Already a known issue they're working on finding a solution for. And it's to improve draw distance for EVERYTHING, not just to buff Swarm Launchers.

Reactive Armour as a counter to "squishing":
Terrible idea. It makes more sense to increase the damage vehicles take from hitting ground, or to apply that damage directly to armour instead of letting shields absorb the impact. Adding Reactive Armour would cause more exploits than it solves.