It's actually the ships that have to spend time repositioning and can't just rush into the fight ASAP that will be hurt. PTL Interceptors and things already have to play defensively to win some matchups. It'll be pretty difficult for those ships to get full wins against swarms and lists with lots of ships/hull, even in 75 minutes.
I am personally not a fan of this idea, because a time limit already forces over aggressive behavior. Now any defensive playing, such as disengaging from a fight, which is the best choice some times, will be penalized even more with not even a full win when time is called and ahead by 12+ pts.
I agree that ships that lose a round or two to re-position are a bit disadvantaged under time limits, but we already have that situation. It's why I say TIE swarm is a bad matchup for dual Aggressors; winnable, but the Aggressor player is disadvantaged for sure (in a tournament setting). I don't see a way to fix this without doing away with time limits altogether, do you?
I admit to a little confusion: you say that a time limit "already forces over aggressive behavior", but there's a thread full of people here complaining about slow play under the current time limit rules. Which is actually the case?
