The “late game tedium” problem is definitely an issue with 4X style games in general - one way to address this would be to apply the consistent race control you mentioned, and to design planetary production so that the focus of fighting a race is wearing down and defeating their main fleet, after which you can quickly mop up - combine this with having distant races get better planets and you could keep the final mop-up phase short.
As for the replayability problems of stock ships - one solution would be for Cliffski to keep integrating the best-performing campaign ships (by saving post-battle stats) into the game and the AI deployment algorithm, until all the races have a good selection of ships.