See, the problem (or advantage) of the option to choose was that it could be 'abused' to totally keep you out of the stupid roaming instances that pull you into a battlefield when you just want to go across the sector.
When one made a beeline towards you, you could just hit the Cancel button that came up on the Choose Instance screen and not get sucked in.
Honestly, I thought it was a great feature, as most of the time I didn't want to go into those stupid things.
Dude give it up. You can change istance whenever you want to by clicking on the map and hitting "change instance". Either way it usually throws you into an instance when you join a map that has your friends/team in it. If you want a different one, its a couple mouse clicks away.
Since the option to change instances is available off the mini-map, I'm not sure it's really necessary to have it prompt all the time... But, I would say that the automatic choosing of instances should have a bit of intelligence to it...
First, when in a team and members are in the same sector, system or map it should ALWAYS put team members together in the same instance. Bad enough this MMO is so sharded to make it feel more single player than MMO, but when you try to play with friends you eithere waste time constantly trying to get into the same instance together, or you end up just having separate play experiences sharing a chat channel.
Second, the instance chooser should also make an effort to put fleet members into the same instance. Don't make instances full of only members of one fleet, some variety is good. But, people in a fleet should really see one another frequently when they are travelling, doing missions, engaging in fleet actions, etc...