Agreed, ai with constructors and anomalies would be interesting. But you'd end up with all sorts of starbases in your territory that you have (currently) no way of getting rid of short of buying or war. You'd definitely have to give players the "remove starbase" option we get from the Ai all the time in order for that to work.
Then again, on higher difficulties, the Ai is unaffected by FoW, so it knows where all the anomalies are anyway. Humans using constructors with surveryors and wormholes is the counterbalance to that I guess.
I agree with you it needs to do "pre invasion math" - but if that math leads to the conclusion that it needs 6 troops to take that planet, it should have the ability to do so - either by loading 1 ship with sufficient troops, or bringing more than 1 ship in a fleet. Currently it can't do either.
If the Ai is limited to 1 transport per fleet, and can't use the population slider, it can send a max of 2.5 troops per invasion attempt. This makes it ridiculously, laughably easy to make planets invasion proof. Some people may like that I guess....but I prefer to play with the same sets of rules on both sides.
As for 1 transport per fleet, it's up to your play style I guess. For the same reason you suggested (fleet strength) I make my attack fleet without transports, clear the way, then bring in a fleet of 2-3 transports with guards in the fleet to protect it. I'm not using the fleet with the transport to clear the defenders. From what I've seen the Ai does it this way as well, so putting 2 transports in an invasion fleet wouldn't have much of an impact.