One suggestion I would like to make, though I suspect it may not be popular with a lot of people is, is to make ships even more expensive, so that each ship will be more valuable to the player. The main reason why I think this would be good is that it makes battles and the organizing of one's empire generally somewhat more manageable. The scope of the game is huge, but that does not mean that each fleet needs to be as large as it is. The same scope can be had by significantly shrinking the fleet sizes (by making ships more expensive and perhaps making them take longer to build). Though this will not of course impress people who have a fetish for seeing lots of ships on their screen at once.

It has been pointed out elsewhere it is often very difficult to select a specific ship or few from a large battle. This is often because there are 50 ships per side and many of them are clumped together. If the fleets were much smaller it would be much easier to move away that frigate or cruiser that is taking a beating (or to better position a few flak frigates near areas that need defence against bombers for instance).

On a larger scale, I think that making the ships more expensive and more valuable will make organizing one's empire much more manageable. With less ships in one's empire, players will have to less frequently: add new ships to different groups, listen to as many messages about ships being built or arriving at a planet, and check ship's health before sending it into battle.

Of course if you did take this route other balancing would need to be done as well. And again, it would not impress people who have a fetish for seeing lots of ships at once. But in terms of the strategic significance, I think that implementing the proposed suggestion would only bring about positive results. The balancing between ships will become much more apparent when there are less of them and people can get a better sense of how to measure up an enemy's fleet against their own. I would challenge someone to give a good reason why having the game with more ships makes for a better strategy game.

For an example, Consider the RTS game Company of Heroes. It has few units per side (and I don't mean types of units but number of units) and works very well. Would making it so that you could have twice as many units per side make it a better game? I would think not. It was a good choice to make units expensive and valuable. I think that there are even better reasons to do the same with Sins (given its great scale).

-By the way I am actually really quite good at keeping track of a lot of things at once in a game (better than most), so I am not just venting a frustration I have over my lack of ability.   

The game has great promise.