I would much perfer an automatic system for it rather then pesky micro management.
One of the reason I really like AI war is its focus on the big picture rather then the little trivial things, in stark contrast to many other RTS (or tactical games really, strategy is such a misused word) like StarCraft. Not that I mislike StarCraft, but I play AI war for strategy
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The fact you can micro mange in AI war if you so want to, thats a good thing, it can on occation get you out of a hairy situatuion, at the same time as it caters to those who like microing everything to gain even more efficieny. I like making a blob of units and crush my oposition leaving the targeting to the units tehm selfs, because, what general/admiral of an army/navy really dictates all his troops on a personal level?
I amdigressing a bit, but my point is, I rather much perfer a generalized system for targert selection over a system where you spesific units directly.
Not that i got a huge problem with it as of now, I just place my claoking squad a bit off from the main fleet. But really, i don't use cloaking ships that much anymore either, ever since the changes to k-raiding.