Regarding Pirates, what would be their goal? If it isn't to expand and to conquer the star system then what is the pirate player supposed to do? (I assume that the goal of playing the Pirates would be different from that of playing one of the regular races.)
Play as whatever is chasing the Vasari--that's the same as adding another race to the game and to then say it's the one chasing the Vasari. The only problem is that the race chasing the Vasari is probably necessarily overpowered.
Less Lag--here here! A Sins-2 definitely needs to be designed to be truly multicore and to have better performance.
More factions--I'm all for another faction or two, but it's easier to say than to do because it would dramatically increase the difficulty with balancing the races.
More ships--what do you have in mind? What kind of a ship class do you think is missing?
Customizable ships--It's an interesting idea but it would take a lot of effort to implement it and would run the risk of totally messing up the game in terms of balancing the races. Also, there might be a risk of the different races ending up having almost the same units. Perhaps each race could have its own customization options. If it could be pulled off well it really would make the game more interesting and add some extra strategy to it.
Better graphics--definitely. I like the Bailknights mod. Of course better graphics runs the risk of more lag. We'd need an option to turn it off if it causes a problem.
I'm not sure I see the value of having custom factions. It definitely would not work for onlne multiplayer.
You left out the addition of new planet types in your wishlist, btw. (Check out the Sins Plus mod.)
I'd like to see Stardock and Ironclad produce a first rate Sins-2 with a much improved online multiplayer user interface, built-in voice comm, better chat rooms, the ability for people with expansions to easily join non-expansion games, and auto-downloading of Galaxy Forge-made maps. And most importantly--end the minidump and desync problems--they are killing us.
