Lets break it down for those who may be having some trouble.
The best piece of advice i can give you, is dont shoot unless there are no other alternatives. A good example is in out of the ashes, when asked to tag the enemy Ship for an air strike. Instead of fighting everyone in the room, you can stay cloaked and stand right beside the Ceph shooting down into the street, tag the ship and then walk off with out having to battle it out for a few minutes.
Grab a Turret. In most parts where you have to battle heavies or shielded enemies their are either turrets before the area, or nearby. A few bullets from one will take a heavy down quick. Though limited to 150 bullets, burst firing the turret will increase accuracy, and if aiming for the head will mean you have alot more bullets for other enemies running around =D.
Slow and steady wins the race. Sometimes waiting can be a great help, often the enemies will move to different locations opening new routes that are faster or less dangerous. Enemies will also clump together in some locations, a well placed grenade or RPG can reduce their numbers fast making the battles (if you see no alternative) much less one sided. Crouching while stealth reduces power much slower, but also makes you move slower. Dont be afraid to sprint when you have to or crouch past a enemy when surrounded by guys.
Tagging your enemies, even in sections with out the suit telling you about it is a great benefit. Even if your not going to fight them the arrow above their heads helps to pin point their locations as they move around sections of the map and makes working out a route between you and your objective much easier.
Attack from behind ;). In all seriousness though, Stealth Attacks, or even grabbing enemies cause 1 hit kills and save valuable ammo, You cant grab Heavies or shielded enemies(given away by their brighter eyes and a flickering red when shot at), But by sneaking around picking enemies off your chance of survival in a critical section will improve vastly. Also attacking armored cars from behind means they have less time to get the HMG lined up, you can often blow up the car and stealth away before the enemy has even turned and spotted you =D
Pingers. Are Painful. But if you can save most of your explosives for them they die very quickly. Dont waste a weapon slot taking a L-tag(unless your in central station). If you search around as your making your way through the game you should be able to stock up on enough C4 and RPGs to take them out. Try going in Stealth when one turns up and let it focus on the Marines, then either go around the back and cover it in C4, or plant it on the ground and try to lure it over it. You can also take them down by shooting the red glowing ring on its back when its facing towards you.
Plan Key moments. During the helicopter fight in the lab, enemies will throw nades and shoot at you from the roof. If you wait a little bit, and pick some of them off they start roping down from the roof, some will drop RPGs making taking out the copter stupidly easy.
In the mission Corporate Collapse, after exiting the elevator you will be required to use a computer. Instead If you place a piece of C4 on the ground at the entrance of the hallways coming from the Elevator, you can take out all the Cell agents as soon as they come in the room.
Lastly some silenced weapons when shot during stealth wont remove your stealth completely. This means you can often take a few enemies out with headshots from close up then sneak off to recharge before taking out the rest. Semi automatic weapons when switched to single fire with a silencer can often take 2-3 shots before they drain your power completely.
Threat Tracker- Found this very useful early on, but ditched it later for the Proxy Alarm. Its good for when your suit is low on power and your not sure if its safe to decloak to recharge. Any bullets coming in will be highlighted giving away the position of the enemy you may have missed.
Proximity Alarm- Handy in close areas with lots of small rooms or corridors, when your not sure about sticking your head around a corner. Though it doesnt pinpoint their exact location, the puck noise will increase in volume the closer you get.
Cloak Tracker- Really only useful at the end when your fighting the cloaking Ceph. Went through the whole game multiple times and this was the only time i met any cloaking enemies.
Recommended mod- Proximity Alarm
Armor Enhance- Though i used it alot through the easier difficulties, i ended up trading it for Deflection. On SS the enemies chew through your armor to fast for this to be of a real use, but each to their own.
Nano Recharge- This is by far the most useful Armor Mod, with the increase health and power regen its usefulness as an aid for your stealth is amazing. Though during unavoidable fighting sections i did switch this out for deflection.
Deflection- kinda the opposite of armor Enhance, instead of boosting the length of time you get, it boosts the defensive bonus you receive. Found this very handy when fighting Pingers as 1 on 1 this power seemed to help much more then Enhance.
Recommended mod- Nano Recharge(stealth) Deflection (fights)
Mobility Enhance- This was probably the most useful, as 90% of the time was spent sprinting from cover to cover, and reducing power usage is very important.
Air Friction- Didnt use this power as to much time in the open resulted in much death. =(
Air Stomp- Same as above, and the need to get close to use this made it not worth the swarm of bullets you would receive even if you manged to wipe out most of the enemy with it.
Recommended mod- Mobility Enhance
Covert Ops- While probably handy in rooms filled with guys, i could crouch and walk straight pass them with no problem. Maybe more useful if you plan to run around everywhere.
Tracker- While probably very useful if you dont want to use your visor all the time, i found that it was better to spend points getting Stealth Enhance.
Stealth Enhance- Probably the most useful Stealth power, but also the most expensive. The reduction it causes in power usage is enough that i could walk around the map section for quiet a while looking for another place closer to the objective to recharge, or observing where the enemies would be walking next.
Recommended mod- Stealth Enhance.