Ok, as I see it, Cortex Command as it's intended to be has two problems right now. First off, it's kinda starved from a resource point of view... if you just blitz straight for the enemy base straight off, there isn't remotely enough time for either player to start digging up gold. And even if there was something stopping this (say, defence turrets starting in bases), you run out of gold to mine pretty quick, and can't really have resource driven battles.

In my opinion, to make this aspect of the game viable there needs to be a way of producing resources... say, somehow the terrain can regenerate, or gold "wells" like in C&C. Some kind of terrain regen would also help with the gigantic holes that tend to be created.

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Second, while bases look cool and are fun to attack, there's no reason at all to have one. Making a brain enclosed underground or immediately sealing off a preexisting base with concrete is better than any convoluted maze you can make.

The only way to fix this is to have a reason for things to move in and out of the base. For instance, telepods, a safe and quick alternitive to strategically useful but risky dropships; also, maybe you have to bring back mined gold to some sort of repository. One or both of those things would give people a reason to make and defend bases.

Other base-goodies that would add to the game- defence turrets, healing pods, ways to repair/replace base modules, doors, turrets, ect, and add on to them after the game starts. It's pretty easy to rip through bases even with vinilla equipment, and after the enemy does your base is pretty useless.

You make good points. Often I've wondered WHY there needs to be access to the brain room. More than likely, it would be in order to transport the brain, to maintain its systems, and other such things.

Also, I sort of wonder about how power works in these bases. Realistically, the base would have some kind of power source in order to run lights, doors, turrets, and to keep the brain life support system going, as well as the brain's ability to communicate with its bodies. If all of this was considered and enforced, then it would make sense for the base to be interconnected in some manner.

Basically, similar to how you suggested, there needs to be systems and elements set up that enforce - or at least encourage - particular base construction rules. As it stands, you can bury your brain in a fully enclosed tomb deep within the earth, with no logical means of support, and no logical means of controlling its units. Adding on these elements would add a considerable level of strategy to the game, since certain systems could then be targeted and disabled, and then would have to be repaired.

Well, the way I see it, Darlos is completely right and some people might want to do it like that. If possible, that would be an awesome gamemode. The main thing is that some people just want to not have to worry about the brain, so what they do is just bury it away and fight. That's perfectly alright and it's actually pretty fun. If people want there to be strategy, they can agree to make it possible if they're playing with a fellow human. In other cases, it's still possible to break through uber defenses with uber weapons. The base busters can easily null the attempt to create an impenetrable base underground. If the player wants to have to look after their brain, they can make it killable. Otherwise, they can just seal it up and have fun blowing the crud out of people. This whole thing is just a matter of preference. If you really want to have to mine gold, you can add some gold modules. If you want to just completely kill the crud out of the enemy forever, you can just spawn a Blue Destroyer and just go crazy. It's all a matter of preference and it depends on what the player wants to do. I do concur with you about the healing/repair pods though. That would be a great addition and make people actually try to keep them alive in order to get there.

Has you said about Healing/Repair Pods, I often wanted something like that. Not just about the gold, but having to buy everything again always is not so good.
Just a Pod like that to repair/heal replace parts would add more importance to a base, because it would need a underground space to stay on (would be easily destroyed on open space of course) and also access to it. So you need a constructed base to be able to make use of something like this. Even tough the player might still want to seal the brain room, he would have to have the Pods base close to it if he want to be able to defend it. I just think the base needs something more than just the Brain.

Soldiers made of flesh, could use the Repair Pods and replace arms and legs with cybernetic parts. The Pod just need a considerable time to repair so to not disrupt gameplay.

Also, I want to have preseted bases I constructed myself to just put on. Part of what makes me don't try a complex base is because of that. On death difficulty you die many times and to keep building again is not practical.

How about a job, you hire slaves and at the TradeStar Midas their labor will make you profit.
Or maybe a generator, you set the build queue, then make it by supplying that ♥♥♥♥ with many miscellaneous scraps, the harvesters needs to Lua-powered so you can create corpses into blocks.

I likey the the base goodies, want.

Thing is, if we get good reasons to have proper bunkers, we'll really need a way to replace doors, minimum. Maybe have a base building option in the buy menu, or something?

OP makes excellent points. I for one build bases on the premise that I perceive my brain to require a base to "uplink" to a control center in my base to control it's units. To be honest this implied reasoning is just so I have an excuse to make awesome, intricate bases.
It would be nice to have a more detailed and possibley game-dependent reason to have a base, such as power generators as Darlos said, and/or body control stations. Having a body control station in the base taken out would mean the brain would lose the ability to control a ceterain percentage of the bodies it has active I imagine, and none at all if wiped out.

Having more things that bases/bunkers do in terms of win/lose dependency would add a lot of depth to what is currently only an implied nessecity.