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.
Well if they find a way to fix the abuse (Although I agree there needs to be a way to avoid those sector space encounters that divebomb you, too) this needs to be put back because it's causing an inconvenience.
Nevermind that people on slower connections (Me, but I'm not being selfish) or older graphics cards hate getting zoned into full places, but come on let us choose instances to meet up with friends/fleet easier. As far as I know, I haven't once seen "(1 Friend/Team)" shown when changing instances. Maybe because there's way more areas in STO, but that part might be missing as well.
Seriously, what's the point of creating a team, or even a fleet for that matter, if there's no means (either manual or automatic) for keeping players together in instances while doing missions??? Doesn't that make the whole social system kind of pointless??