1) Replace dialog pop-up windows during encounters with flashing alert bars at the side of the screen.
Easy enough to do, as it is already in the game (sort of). If you minimize or chose the "Not now" option, the pop up window automatically gets turned into one of these alert bars right now. Why not have the alert bar be the 'default' setting instead? I mean we would know we have a new message, because we get a 'hailing' sound and a happy flashing bar. We don't need a giant window popping up in our faces. 'Cause there nothing more irritating than completing an objective in the middle of combat and one of these windows pops up while you are getting beat on. Really, when did we see a window pop up covering over most of the characters at the end of a Star Trek episode, while they were in the middle of a closing quip, saying "EPISODE OVER".
2) With the very welcome addition of ship interiors, how about putting them to use?
I for one would love the option to actually use my transporter room to beam down to a planet mission or to a starbase. I'd love the option that when ever a dialog box giving me the choice to beam down some where came up, that if I answer yes, I would be placed in the transporter room. From there, I would chose my away team and they would show up on the transporter pads. When I was finished choosing them, then I would hit the 'beam down' button. (And as an aside, I would like the option to arrive in my transporter room when I beam up too - and that 'visit the bridge' would be 'visit the ship' and I would go to the transporter room instead of directly to the bridge).
3) Speaking of interiors, how about moving sector space to the navigation console on the bridge?
As many folks have said, the sector space mechanic is very un-Trek and unrealistic for space flight. However, it is a beautiful artificial navigation interface. Let's "make it so" by having it open up after clicking on our 'con' station.
4) Bridge viewscreens.
Many threads out there already giving great ideas about how to use these for a more Trek-like experience. Boiled down - when I get a hail from another ship or planet, I want to see it here, and not in a 'pop-up' window. 'nuff said.
Note: all of these are "options" that folks should be able to toggle on or off depending on their preferred playstyle.