In addition, I'd just like to remind everyone that I'm in favor of supply ships and supply yards instead of regenerating AM in ships. So spamming the specials would be harder as the AM wouldn't just come back unless you had enough supply ships that phased in with your fleet.
I'm in favor of something the devs already said wouldn't happen (except in a mod), so that'd make this idea even better than it is if it happened!
... rofflecopter.
Anyway, I personally like the "spamable" nature of most special abilities. Stuff like embargo and the Kol's shield boost wouldn't be effected as long as their length was increased appropriately (as things stand, you can keep an embargo up indefinitely if you don't use anti-matter elsewhere, and I believe the same thing goes for the shield boost). Other powers, like the intercept, repair, designate target and shield restore powers just about
scream for being spamable, they need that to work as they do.
Other stuff, like the anti-matter sabotage power of Cobalts might do well with your new system, while others, like the Kol's direct fire ability would become overpowered if you increased its strength to match a longer cool down.