The downside is a more UI, more complexity (including for the AI) and more difficulty for the player in comprehending the potential ranges of his ships at different speeds. The question is whether the game play benefit of having cruising speed is worth the complexity.
I think KISS would be to add an overboost or 'afterburner' mode to engines; similar to how spinals bump the focal size up, overboost rating just boosts the engine power VS efficiency rating up a level or several(maybe research dependent, set in the engine design), but probably with much worse efficiency than would normally be expected(say power goes up by X levels but efficiency loss is 1. 5 or 2x that or something); thus a ship gets a standard and overboost value for speed and range(and thermal sig; a overboosting engine is probably much hotter than it's engine power would suggest), and you have to decide if it's worth investing the research into boostable engines in addition to deciding of it's worth the fuel to use them; not just for speed but also the boost to evasion VS enemy fire.
Simple, straight forward, and uses existing mechanics and concepts already in the game.
Also, I haven't been able to find an answer either way as to existing C# mechanics/plans, so apologies if I've missed it, but I'm hoping atleast some ordinance weapons will be able to do damage in space combat, even if it's really short range and low damage, for consistency and roleplay; I know you can build multirole fighters by putting ordinance pods into box launchers, but it'd be a bit odd if your air superiority fighter can kill enemy fighters all day, but once it's above the atmosphere it's weapons stop working. And I like the idea of planetary fighter wings launching a desperate counterattack against landing troop ships or a standoff orbital bombardment or the ilk, rather than being completely helpless. Probably a long shot, but maybe something for the future.