While making it open and moddable goes without saying, I would caution against releasing something largely dependent on the mod community to 'finish the project'. I beta tested Star Rulers recently...a lot of really cool stuff under the hood including some of the things others are talking about here .....like ship design of any size along with some other novel ideas. However, the game just didn't feel complete to me and since I am not a modder, I never purchased it.
The concept of the huge universe versus increased detail at the solar system level really makes no difference to me. At the end of the day you will be trying to strike the right level of 'things to control' and 'things to manage'. In my mind what is important is how the user manages the empire ... whatever that may consist of. So many games seem to fail on this point, while the kings of the genre have done a good job in this area. Though not perfect, Gal Civ2 and Sword of The Stars have done a good job in this area. An out of genre example of a decent management interface is Dominions 3. Star Rulers provides a rich and detailed empire...it simply forgot to code a good interface.. I think this is an important point because if its difficult to get to where you need to be issue builds, orders, etc... you lose potential market right up front no matter how cool things are 'under the hood'.
On Tech, I like the idea of RP and EP. It's along the lines of what Hearts of Iron 3 did with it practical knowledge versus theoretical knowledge. It makes sense. That coupled with a somewhat randomized tech tree works for me. I liked what Sword of the Stars did. Here you have all races being able to research basic tech, but as you go up a particular tree you have a percentage chance of being able to research the next item in the tree....each races percentage chance is different. So Race 1 may have a 90% chance of getting the next level in a tree, while race 2 may only have a 40% chance. So though you have a general path that works better for your race, each game is different because you might not get that whiz bang tech you depend on. I also like the idea of a series of techs that are outside a standard tree but may discovered randomly under certain conditions...kind of an unplanned breakthrough.
On combat .... I am torn. Regardless of which way you go, it has got be physics based combat where ship components, placement, and overall design become meaningful. I like the concept of Gratuitous Space Battles where you setup AI and the fleets fight it out, but it might not work well for a large scale empire game where you have tons of fleets to manage. Unless....interfaces for putting together AI 'scripts' and attaching them to ships and fleets was easy. Barring that, the turn based strategy and real time combat of Sword of the Stars is a winner in my book.
On ship design .... I love it and look for this to be a well thought out and unique experience that results in lots of meaningful variation.
While I would like to see the emphasis on ship building and combat, you might give some thought to have some rare strategic resources that are only found in certain systems and required to build certain components or perhaps even to allow discovery of certain techs.. I find many games in the genre, though they have different resource levels and possibly vary in how easy to colonize, look pretty much the same once terraformed and industrialized. I like the concept of somewhat unique systems where controlling that system .... and the SPICE it produces
becomes a key system to fight over.
On officers and leaders ... They seem better suited for colony and system management than as fleet commanders. While we can all appreciate having a James T Kirk, how much impact will the man have on future space battles which will effectively be fought by computers and systems. Maybe the Fleet AI Programmer gains in level and can code more advanaced routines?
Anyway, my 2 cents...Good luck lads!