Excellent ideas, as always Syndrix.
I too was disappointed with the way choices were done in JK. As for level fluidity, I hope they do something similar, but slightly different from Half-Life. I hope they take all the levels next to each other on the same planet and make them one huge level, with an in-game loading whenever you reach a different part, this way, gameplay won't be super slow. Then, when you're done with that planet, there's a short, in-game cutscene of you're ship jumping into hyperspace, either from cockpit or outside view, and then you take a break and see how you did, with another in-game cutscene of the aftermath.