i think towers and factories can be predefined and cannot be built again! so that the player cant gangup just the towers and also will have to put some kinds of activation (switch?) on towers so that they can be activated when required by paying up some energy?
Never seen something like that on a tower defense game, and... let's say that I think that would make the game un-playable at long terms.
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For something like that, I think the general idea is much simpler:
Try to visualize the situation:
A map with two separated bases. One contains an HQ, the other, one or more factories.
The base with the HQ is controlled by the player, who can construct defenses without the need of a truck.
The base with the Factory will be controlled by the Computer (or another player), the construction of trucks, not possible to this one, so he cannot make addittional structures, only units, which will go attacking the HQ or the defenses.
Both bases will have one or more research centers, and a constant income of energy resource, so both sides can improve as time passes (like on any standard tower defense game).
Last detail, maybe this gamemode, mod, or however you wanna call it, would require an specific rebalance, having in mind that both sides should always be in fair balance.
I dunno how hard can this be to implement. But I think it's the correct way.