I think that a system to swap out ship's countermeasures just like missiles and guns would be a good idea at this point. That, and have CMs support automatic burst-launch and substitution. Would add yet another factor to customize when gearing up the ship (not to mention burst chaff+flare launch would look really cool).
For now, it'd be good to see some variety between different races. UEF, GTVA, Vasudans and (eventually) Shivans and Vishnans could each have their own flares, with actually different stats, not just different visuals.