As most players know, the empire tree is supposed to make ship organization and giving commands easier. However, especially in larger battles, ships are either dying, leaving, or entering the battle so quickly that reliably selecting a ship and giving it a command from the empire tree can be very difficult, if not impossible, because the ships displayed jump around so much. Short of a serious redesign of the whole thing, I have an idea which might go a long way towards making the empire tree much more usable: enable an option to register ingame clicks on select, instead of on release. As it is now, clicks seem to always registered by the game only after the button is released, and then the game seems to often wait until the next tic or so (more if there's lag) to display the ship as being selected. If the empire tree has moved even a single ship during that time, there's a great chance that you'll have failed to select the ship you want... and your failure to select that ship could make a significant difference in battles, especially if it happens more than once, which is quite likely if fleets are of a halfway decent size.
However, if you know that if you press mouse1 over the particular ship you want, that the ship will certainly be selected when the next tic rolls around, using the empire tree would be significantly easier; it would be much more reliable. Even if it does jump around, if you can be satisfied that a particular ship selection will be successful after finishing a click, it would be much better.
A semi-related problem is that, on ICO, commands are only displayed to you after the server registers them, so it seems. If I tell a ship to attack another ship, there seems to always be a small delay, which is most likely due to lag, which is not present on single player games. Sometimes though, an attempted command doesn't go through to the server reliably despite pressing the correct buttons, meaning that I have to babysit my ships for a couple seconds every single time an order is given, just to make sure the order goes through. If Sins displayed orders to the player as having been given immediately, it would solve the problem: of course, nothing would actually happen in space until the server responds, but at least one wouldn't have to wait on ships to make sure they're know what their future orders are.
Fixing the Empire Tree is much more important I think, but any acknowledgement (or fix) of either of these issues would be great.