well, here it goes. This is from a marine's point of view, instead of a normal commander.
Marines like orders. And not stupid orders either. I feel that I should be DOING something useful when playing, and standing at the base is not useful. However, if the base NEEDS someone standing at it, that is a different matter entirely. So, if you just want a guy to pull guard duty on an outpost or act as a sentry/early warning for your builder crew, SAY SO.
Next, learn names. Nothing is more annoying than being on an 8 man team and being told "two guys go to water filtration". Marines really don't know where all the other marines are, or what they are doing, so give names. Pick two guys who aren't doing anything important, and give them orders to do something.
After that? Don't waste expansion money on guns. Heavy armour marines are nice, but so are resource collectors. Standing for 20 minutes at a resource node waiting for your commander to stop buying heavy machine guns with every dollar your team makes when you could be increasing your income is also tiresome. Also, NEVER EVER EVER give a gun to a marine just because he asked for one: it undermines your authority, and wastes resources that may have been spent better somewhere else. If one asks for a tactical item, it is worth listening, but being a slave to all the rambos out there that want hmgs at all times is the path to defeat. For a harassing troop that has shown himself to be competent with a pistol, a grenade launcher can be considered tactical. Laser mines are tactical. A welder is tactical (and is well worth considering: a marine who cares enough about fixing something that is damaged instead of just killing will be likely to protect your investment). Never feel obligated to give someone something just because they want it though: The pistol does more damage than the hmg, and it is very important that you use your limited omniscient perspective to make decisions for the good of the team.
Senty turrets: try to spread these out some. A wall across a base entrance is all well and good, but you should make sure that when designing any base, there is no single point anywhere in the room where a skulk can stand and attack either your turret factory or your command center: these two buildings are vital, and you should make sure that to get to them, your opponent has to level the entire outpost. In my opinion, the patch went a little TOO far. aliens are fast enough that they don't really need the effective base defense to the same degree as a marine, and marine buildings are a lot harder to repair (and don't heal automatically, last time I checked.) Sentry turrets shouldn't be the be all and end all, but the turret factory weakness is a little too easy to exploit.
Also: spread armories around. As a commander, your time is valuable, and you should avoid wasting it wherever possible on restocking marines. In addition, with more bullets, your marines will be a LOT more aggressive in combat, and therefore more effective. Marines with low ammo will only really shoot when it is a matter of self preservation, or when they have a very high likelyhood of killing someone. With more bullets in the air, the sheer likelyhood of tagging aliens with stray bullets increases dramatically, and also makes the aliens a lot less agressive (I should know, I spend a lot of my time playing an alien

) Given that restocking at an armory is free, there is no real excuse for only having one armory on the map. If it is not practical for a marine to walk back whenever he needs ammo, and he will be spending more time in an area it takes him to walk through it, an armoury would likely be a good investment. In addition, when you are ready to upgrade an armoury, your troops can go elsewhere to get more bullets.
If you see you have a superhero marine somewhere (i.e.: one that can aim), try to drop health packs for him when it is convenient for you. If you can' drop supplies whenever you can, but it isn't your most important job: if you have time, do it, if not, just make sure you always have an infantry portal. Don't get mad at your team if they can't hit an alien either. in close corners, with a 50 shot clip, against an alien that can take a dozen shots before going down, you might have troubles too.
Next, learn where the hives are, and build outposts at unoccupied hives quickly. An onos rush (by competent players) is game ending. period, and bile bombing fades aren't much better. The effectiveness increase between two hives and three hives is huge, and even if there is nothing of value at a hive location, it is worth setting up just so the aliens can't.
finally, a note on waypoints. Last, but far from least. A marine really doesn't know what's around the next corner. Try instead of telling a marine to go stand beside the hive to harass it, send him just outside the door, and let him figure out why he's there. If you give orders that are humanly possible to achieve, people will get used to following them, instead of ignoring you, and no one likes suicide rushing alone. Give a marine a pair of friends to go attack with, and he won't mind if he gets overwhelmed too much, but being told to attack 3 onos, 14 offese towers, and a fade at the same time is annoying. It means your commander doesn't have anything better for you to do. Which means he doesn't really have any long term plans for how he will win the game. Marines win by Going out, establishing some ouposts for resources, controlling AT LEAST one hive location, upgrading to the nines, then sweeping the aliens off the map in combined teams. Never forget this, and if you ever lose your compass, think about this plan, and decide what you need to do to get back on the track. In rts games, a lot of people start getting lazy and just slugging it out with wave after wave of badly executed attacks. To be a good commander, you have to be micromanaging as effectively as you can be at ALL TIMES, not just during the start and endgames. If you want to take an occasional nap at your keyboard, play a marine or an alien, and request guard duty

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