You grossly underestimate the addition of the civ-unique tech trees. That added no new top-level UI to micro-management but added respectable variety to the game. I was stuck in a deep Thalan rut for ages, but TA got me regularly playing as Arceans, Altarians, Iconians, and Yor.

The asteroids were a final disappointment to me. But I like 'good' micromanagement, so I wouldn't agree with you that they're a useless bother if the devs had retained the idea of assigning an asteroid base a role (I'd have enjoyed 3 flavors: production, research, or cash).

The espionage problem charon2112 describes seems to be a play style thing. It almost never happens to me because I tend to stick to the middle of the power-ranking pack on very large maps until well into the game. By the time I'm strong enough to start attracting heavy espionage attention from the AIs, they've burned most of their assets amongst themselves and I have a fat stack of reserve spies to zap the occasional intruder.

Yep, and sometimes the notice (to the right at the screen) that a planet has been infiltrated by an enemy spy lags for a turn or two.

And ships sometimes circumvent asteroids, sometimes not, it's a mess.

I'm pretty sure that the whatsis-blocks in the map window consistently report late on enemy spies. Whenever I notice an espionage wave starting, I check the Espionage tab directly before ending turns. You can kill enemy spies from there and then see them reported in the whatsis-blocks at the start of the next turn; follow the block-link to the planet in question, no spy.

Re Counter Espionage Centres, their value also is probably affected by play style. I almost never feel a need to build them, have maybe done it three times in tens of gigantic and immense games, and then only on very large worlds that seemed to be unusually attractive to the AI spymasters.