Use sync shots. It's a great way to eliminate enemies silently, especially given how the bots never miss. This will enable you to complete some missions without firing a single shot. Invest your first skill points in sync shots. You can have up to 3 of them.
Use the drone to spot and mark enemies. Things look better from above, not to mention the fact that you don't have to risk your own life. Remember that you can use sync shots while controlling the drone.
Look often at your TACMAP. Enemies are marked with a red fade. Once you mark them, it will change into a red dot. If you see a lot of red, mark enemies until only dots remain.
Use the right weapons for the right battlefield. If you're going on a stealth mission, equip yourself with silencers. Automatic rifle + sniper rifle combo works pretty well. If you intend to engage your enemies directly, pick a weapon with a large magazine, which you won't have to reload very often, such as an LMG.
Collect resources. You can use them to develop your characters. You'll find them in all missions. Just take a walk across the battlefield after the mission is completed and your supplies will be replenished.
Keep yourself supplied in ammo. Ammo crates a located in many places, but somehow you can never find one when you run out of bullets. Resupply whenever you can, and make sure you always have your pockets stuffed full.
Watch out for grenades. The dangerous area around a grenade is marked with a red field. To avoid health loss, try to keep yourself outside of it. And don't forget to return the favor. Just throw them grenades a bit farther than under your own feet, ok?
Eliminate enemies beginning with snipers and scouts. You'll find them on positions with a good view of the battlefield. To take down a sniper you don't have to come close. Use your own sniper rifle or a sync shot.
Use rebel support. It's free, and the rebels can save you as much as half of mission time in some cases.