The biggest problem with this (at least for me) is where do new ships appear at my starbase. Let's say an enemy bomber is heading for my station at the start of a game. I have just enough money to buy a scavenger. If that scavenger appears at the corner that is the exact opposite to the direction where the enemy ship is approaching from, it will have to travel an extra sector when I send it to meet the bomber. This might (and has) mean the difference between the scanveger destroying the bomber before it reaches my starbase, or the bomber reaching the base and fireing one shot at my station before being destroyed. That's 10 hitpoints lost and possibly losing the 5$ scanvenger bonus because the starbase destroyed the bomber while the scavenger was still in the other sector

This has happened to me several times, of course not always with bombers, but often at the start of the game the enemies send single ships that are hard to take out due to lack of ships.
What about this: Let the player choose which quadrant of the station new ships appear if there are no ships stationed at the starbase? A simple method could be selecting the starbase, and then right clicking one of the corners of that sector. You could visually verify the selection with the standard green "move-here" dot, and maybe add an arrow or a single corner marker or something to that corner for permanent display. (To clarify that: a claimed planet has corners in the players color around it. Draw a similar symbol to the chosen corner)
What do you think? Shouldn't be too hard to implement, and this could could really help get out of sticky situations when the enemy is approaching and you really want that new ship to get out there fast.