Not sure if there is an alternative to doomstacks. IMO what you can do is either make battles last longer or make fleet movement slower (maybe increase speed Penalty with increasing fleet size - obvious Counter to that is just split your Forces just to Combine them again at destination) so skirmishing and harassing economy becomes viable. At the same time make defensive structures stronger so doomstacks are not replaced by even more annoying base trades.
But all in all I agree with People saying doomstacks are just the RPG ish result of an empire's Upgrades, traits and strategic resources. This is not a Micro oriented game and never will be, hence the above listed Options are more strategic than tactical.