Well, Space does tend to be open like that. 
I do think it would be an interesting mini-mod. Might even make 1v1 games rather ...different. 'Open Space' would just be cool, even if annoying in its ways as you say. Though that might be fixed with increased resource rates and Tactical slots, but if it only works for the owner of whatever used the ability, then there goes that idea.
And, I did not want to give it to the AI Raider-Pirates, that would be horrible. 
I was considering making a Pirate faction as a fourth race and giving it to them as a research or such.
So I was looking into that, and not knowing how to really mod the game, I cant seem to find a way to add ship-like abilities to planets. Then while looking up random mod info about such things, I ran across this post by JA_394 here.
Which said:
"I've got an idea: What if you gave the specified ability to the faction specific construction ships? Those are always there and when you conquer a planet, one immiedietly shows up."
(Sorry, I dont seem to see a 'Quote' button in the quick reply. I'm sure I've missed it, but yeah.)
Anyways. Duh. >.<
Give the Phase Scout ability to the Construction ships instead. Then all the actual planets you control would have a 'Phase Beacon' or whatever you want to call it, and all your ships should be able to phase jump to any planet you own. (Unless the Construction ships located there are destroyed or something. Which gives an argument to making it a planet ability instead, but I have no clue how to go about that.)
I'd still Really like to be able to figure out how to make it a more or less 'Open Space' ability.
Also. Wouldn't the AI have scout your home planet, or any planet, before being able to send ships there? 