Did the war mechanics change in a patch? I am waiting for beta 5 to restart a game and haven't played for a bit.
If not what's stopping you declaring war? Just go into diplomacy with that race, then declare war. If it's a UP resolution which I haven't seen yet, can you leave the UP if you want total control yet (also not something i've done yet).
It's a beta however, so the game certainly has issues, and will continue to have issues until release. As for limited choices, you have diplomacy, ideology, technology choices, ship design choices, planet choices, starbase choices, galaxy type choices, victory condition choice, moddability, (and soon custom race choices as well as minors). You have a lot of choices in this game, much more than most i've seen or played, but then that's why I play it.
The AI is weak in beta 4 for example, in beta 5 it will be improved, if you want more of a finished game, wait until that one hits, but even then it's still a beta until it's not anymore.