I know making RTS elements and city building can draw the developers away from the main game, but does it matter? It is more or less perfection as it is already, so there really isn't much point improving it even further. But of course, that's no reason not to try.

As for the Deathstar, it might and might not work. The last thing I want is the game to end as soon as someone gets one. I would rather have the option to build a huuuuuuuge battlestation instead of a few dozen normal ships. Basically have the firepower of an entire fleet in a single unit. Here is how I can see it working:
* Being planetsized, every single planet in your empire needs to work together to create a Deathstar. This basically translates to if one planet starts to build it (your capital only, perhaps?), every other planet will put their ships on hold until the deathstar is finished. In other words, while you will have major firepower once it is done, you will not really have any until it is done. Except if you make a fleet or five first, of course. But that will take even longer, so you can't really focus on anything other than firepower. And by the time you have your deathstar operating, you could easily have lost thanks to influence, technology or something else instead.
But let's say you did get a deathstar. Have you won automatically? By all means, no! It just gives you an advantage... unless, of course, someone else successfully infiltrate it and takes it away from you. Suddenly your ultimate weapon are turned against you, so what do you do? Either do everything you can to make friends with whoever owns the deathstar now, or try to take it away from him or her. Or, of course, sabotage it and blow it up. There's always another possibility. The bottom line is, I want a Deathstar that gives you the firepower of an entire fleet in a single unit, but at the same time it can not be too powerful either.
As for Wonders of the Universe/World, I haven't played enough to find them. Or I did find a few, but every single faction seemed to get it directly after each other, so it doesn't count. I'm talking about wonders that gives a great advantage to whoever owns it. If you build one, I can take it away from you and get the bonus for myself instead.
And yes, the governors. Some might like them, some might not. But the idea was to let the player choose what he or she wants to focus on and have the governors do the boring rest. Do you really want to make sure the population is happy instead of going to battle with your newly created battleships? Bomb the enemy planet, or create another research facility? Easy choice, really. And of course, the governors are all optional. If you don't want them, you don't need them. If you are in a boring phase like early in the game, let the governors take over while you go eat dinner or something. Just make sure you have activate Auto Turn, so the game skips a turn everything there isn't anything to do.
And as for the city builder, I'm not thinking about a city for every square on the plane map. I'm thinking more of a single city, perhaps your capital. Most cities in your empire will be the same anyway, so it's just tedious to micromanage every single one of them in a city builder. But think of the Palace in Civilization. If you make a great civilization, your people will be impressed and hand you a palace you can design. Why not do that in GalCiv3 as well? If we have city like this, said city can have a lot of things the other cities don't. Your own palace, perhaps a Wonder (like the pyramids, hanging gardens etc) or whatever. Just thought it could be fun.