1) Make capital ships NOT use any fleet points. Just Capital Ship points.
https://forums.sinsofasolarempire.com/324591
There seems to be a general concensus that there really isn't any reason to build more than 1 or maybe 2 capital ships. Why then are we allowed to build 16? Nobody would ever do that. They're too expensive considering what you get. Not only do you have to pay the expensive cost, but you must perform the extreamly expensive research beforehand.
If Capital Ships didn't use fleet points, once a player has maxed out his fleet he would have a choice, go to the next fleet level and start paying 9% more in upkeep, or he can build a few Capital Ships. Overall I think this would add a level of diversity to the game (particularly the multiplayer). You might actually see a skilled player using more than 2 capital ships.
Edit: In other words. Capital Ships would have the added incentive of NOT raising your fleet upkeep. Perhaps then they would be more attractive for the cost; which is already high enough.
2) Interest.
There is currently no reason to save resources. If there were to be a modest interest applied to the resources you had, then there would be a reason to save. Say you had 10,000 credits, you may get an extra 10 credits per turn in interest.
Again, this would add diversity to the game (especially multiplayer) you could spend spend spend and develop military might. This could give you the upper hand if played right. You could also stockpile your resources and gain some interest, ultimately resulting in greater income. But when things get tough, you'll have to decide wither you want to turn that stockpile into ships, and say goodbye to the interest, of hold on the to stockpile and the added income and hope you can make due with the ships you have. This could potentially speed up the multiplayer a bit, and would help provide income at higher fleet levels. It would have to be balance, but if done right, could add a new level of depth to the game. This is supposed to be a 4X afterall.