[Will]

Some comments....

Facility that adds facility space to a planet

You DO realize how unbalancing/unrealistic this is, correct? Maybe if there is a one per planet restriction...

When viewing a system show what ships and colonies are in the system the Last time the player could see it

If this is put in, it really should be set to off by default. Not everyone has the luxury of game files in excess of several megabytes. Even if it's just limited to storing the ship class/planet population, that's a lot of extra data to keep track of for each player.

Save kT destroyed for individual ships instead of just class

File size, but not as much as above... only 4 bytes * total_ships, but still, for such a trivial thing... ship experience is a good enough indicator of this.

Show the damage to ships in combat replay for simultaneous game

Ok, for this one, you're talking huge combat files. Right now, the game only has to save movement coordinates, firing targets (and whether the shot hit or missed), and ship damage at the end of each combat turn. This would require saving the component hit for each shot and if it's destroyed, as well. The file size increases of the Last two would be trivial compared to the hugeness of this if there is a big confrontation.

For those, IMHO, the "benefits" (AKA "coolness factor") of these updates wouldn't help gameplay significantly, and would add restrictions to some Users. You have to remember, not everyone has high bandwidth or insanely huge hard drives.

For the rest, nothing immediately comes to mind on potential problems, other than varying degrees of coding effort. And, since only one person (perhaps a few others) knows anything about the SE4 source, I can't really comment on difficulty