Given that there are so many players who seem to be happy to play with time having only a small cost and running things mostly at their own tempo (despite whatever the original design intentions were for the price of time), even if they occasionally complain that they feel they are forced into netflix mode, and given that there are already many options that can be enabled to make time costlier (auto-AIP and mining Golem being the biggest), I'm not so sure that the game needs to be changed such that time is costly as default, so much as it needs to be made more in-your face in-game at all times that time
does have a cost, whether it be great or small, something that is not viscerally felt with the CPAs that come so far apart.
As one possible outrageous suggestion for how to accomplish the latter, and I say this solely because I am evil and deliberately not thinking about the implications for the poor CPU, have a DefenceFactor present at all times in the top bar of the main display (e.g. DF 1.23). This factor is then used as a multiplier on the maximum number of ships that will be used to guard any planet after all other considerations have been made, the maximum size of the special forces (poor CPU, this might be a killer), and the maximum size of reserves the AI will accumulate. Have it start at 1 with lobby options governing its growth, say 5%/hour as the minimum setting, with some higher value recommended, and update the displayed variable as the DF is increased, either two or three digit precision so the player will be reminded all the time that the DF is counting up.
Since the DF is only used for defensive purposes, the AIP remains the dominant factor where threat to the player is concerned, allowing the player to remain in control of the tempo where his survival is concerned, if that's how he likes to play. What it
does introduce, or at least what I would hope it would introduce, is a feeling in the player than whenever he takes his time forting up and preparing, so too does the AI.
Downside? It would make 200h games as that mentioned earlier in the thread rather difficult to win.
EDIT: You know what? Upon further consideration, I hate this idea. Introducing another variable to keep track of, and one that is fairly boring as it is outside player control and slaved to the clock at that, would probably end up more annoying than helpful. Oh, well, that's the danger of rapid development ideas unconstrained by mental review - at least nine out of ten of them are crap.