Use Grenades
Grenades can turn an overwhelmingly difficult battle into a surprisingly easy one. Using a hedgehog grenade before entering a room, for example, can help clear out the area or at least severely weaken any enemies in there, making your job much easier. The air-fuel grenade takes a while to explode but is extremely potent against immobile objects that are difficult to get by.
Keep Weapons Basic
Although you will receive many different guns throughout the game, the first two you get, the M5A2 and the Bullseye, are the ones you will want to use the most. The M5A2 has nice accuracy and can be used as a poor man's sniper rifle, while the Bullseye has a high firing rate and does significant damage, making it a potent close-range weapon.
Basic Battle Tips
Always stay on the move -- even in an area where it appears there is nothing around you, you should always be shifting your position side to side to prevent an enemy from picking you off easily. When you do confront an enemy, make sure to shoot him in the head to both preserve ammunition and to take him out much quicker.
Use Hidden Weapons
On a second run-through on a harder difficulty, you will have access to five new weapons: the arc charger, the backlash grenade, the L11-2 Dragon, the reaper and the splitter. Although the arc charger, reaper and splitters are not especially useful, the L11-2 deals out instant kills often and the backlash grenade will repel Chimera weapons, enabling you to turn the tide in battles where you may be overwhelmed in numbers.