A few suggestions which will probably make the game more challenging:
1) A military starbase should have the capability to automatically attack or engage all enemy ships that enter its sphere or circle of influence. Right now, starbases to me seem useless. Sure they help the economy and provide influence and all that other stuff, but in a war, I don't even bother to engage the enemy starbases. It is a lot easier just to bypass all of them and attack the enemy planets directly. Oh sure, you can attack the economy and influence starbases and wear the enemy down slowly, but why bother ? Attack his homeworlds, knock him out, and the starbases just disappear once he is conquered anyway.
Something that would enhance the game would be to give the MILITARY starbases the ability to auto-engage any ships entering its sector (or that red circular sphere of influence around a starbase). Now you have to plan a strategy for either attacking a starbase directly to knock it out. And if a player surrounds his core worlds with some military starbases, it becomes a trickier situation to take his planets, because once your ships move to the planet's location, they have no choice but to fight the starbases first. Also, now a player can actually put a MILITARY starbase next to an Influence or Trade starbase to protect it better. I would not give the ability to auto-engage to Influence or Trade starbases (to preserve balance a little more).
Now players have more of an incentive to research the Starbase Defense and Attack technologies since Starbases can play more of a role in defense of territory and homeworlds. The current Military starbase assist stuff (i.e. The tractor beam, weapon assist, etc.) all seem pretty pitiful when you consider that they can only assist fleets in the area, and enemy fleets that are fast can simply engage the planet in an attack during one round of play, wipe out all the ships that might be stationed on the planet, and then land the troop ships in the same round - totally bypassing all the starbases in the sector. BUT if I had no choice but to be forced to engage military starbases in that sector first before any planet could be attacked or invaded, I would Certainly think twice before I did that. This would also give the weaker races (and the minor races) a better chance to last longer in the game. I hate being at the beginning or middle of an empire and technology buildup, only to have a weaker race give up and surrender all its planets to the evil bad attacking guys so easily. I mean come on! I have been in games where the "weaker" race being attacked had all kinds of starbases and fleets of ships out there and then all of a sudden, they just give up. What is up with that ?
2) Minor races - It seems the only reason for being for these races is to colonize a planet that was previously class 0 or 1 or 2 and then it immediately turns into a Class 15. Then almost like clockwork on the next few turns, one or more races go to war with the minor race. Usually very few battles occur (well duh, the minor races don't have fleets), and then they surrender and the attacker gets a brand new Class 15 or higher world (usually in territory that I control too). The minor races seem to come along later in the game after only a few major races are left, and all they seem to do is construct stuff - minor starbases and the like. Why not just have them become new major race replacements ? Instead of colonizing a single planet in a star system, let them be able to colonize an entire star system (all 4 or 5 planets), and then act just like a new major race ? It would be more challenging, and assuming they act like a major race, they would build fleets and would defend themselves and their turf accordingly. No more pushover minor race / get high quality planets for bad guys freebies! Besides ! I like the Scottalingas ! I could see an alliance with that Walter Scott guy !.
3) What is up with the charges for building some starbases ? For example, I usually play the long games (large galaxy, lots of stars, lots of habitable worlds). I build 10 or so starbases - they cost nothing and my logistics capability can support them. But as I get around to building more (still within my logistics capability), it starts costing money to build a starbase - it starts out small (few hundred credits), but around the 20th or 25th starbase, it runs into a few thousand credits to build a new one. Is this a bug of some sort ? I'm not talking about module costs either (like the 100 or 200 bc for adding BattleStations capabilities either) - I can understand those costs and am okay with those.
4) How come Starbases have such lousy hull points for taking damage ? I mean it seems the max you can get after loading up battle stations and other defensive measures is a lousy 48 or so hull points. Given that most starbases are going to be much larger than starships, should they have something like 100 or more hull points after you load them up ? The 48 hull points just does not seem to be enough. If you want to compensate by making Starbases cost more, or creating a new "Hull Strengthing construction upgrade" module that costs a lot of money, that is okay, but starbase hull points should not be so low.
5) Eyes of the Universe - this should be enhanced slightly so that planets you own also get to dispel the "fog of war" for the same radius as your ships and starbases.