Agreed with all of the above. Now that you mention it, the diversity does create a gap in relating and also in the feel between the two trilogies. As I created the thread trying to tie the two closer together, simply replacing many of the aliens with humans would go a long way.

That said, I also agree that the difference between the trilogies makes sense, considering the xenophobic Empire (at least according to EU sources, but it makes sense). There would be a lot of aliens in the Republic when contrasted with the Empire. I always found the end of ROTS to be a little startling because we were supposed to see a transition from Republic to Empire, but it feels rather sudden when Vader and Palpatine are in their star destroyer staring at the Death Star under construction. The ship design is all of the sudden familiar, but I never realized till reading this that the fact that there are only humans on board the ship also creates that same sense. It really was too drastic. Perhaps some hint at Palpatine's purging of aliens from the ranks would better serve the transition and better get the feel you are aiming for.

And with that, I agree with the last comment that his advisor should not be an alien given his apparent xenophobia.