The beaming makes sense for visiting captains, and they probably haven't figured out how to make it different for the player that owns the ship.
The BIGGEST thing that needs to be done is the uniforms. I agree that a seperate uniform for each crew type (eng, tac, sci) should be available. There also needs to be male/female specific uniforms for each type, so I can put the girls in skirts and the guys in pants. It doesn't feel like MY ship with a bunch of randomly uniformed NPCs walking around.
I would like to see functionality added to the ship interior before they work on any major customization features.
I like the ideas of the minigames like poker and 3d chess. That would be awesome. The holodeck is another great idea, there is so much that could be done with one on your ship. The fleet and personal banks should really be added to the cargo bays, and you should be able to check your mail and the exchange from your desk in the ready room.
As far as customizing the interior, the priority should be to change the ship schematics on your LCARS to your ACTUAL ship, not just a random canon class ship on your bridge. I would also like to see a ship's plaque on the wall with the stardate of luanch, ect. of the specific ship, with an option to add a ship moto.
Layout according to size is fine with me the way it is broken up into large/medium/small sizes, but the interior should really change colors with your bridge. That would go a long way to full immersion.
Once the above is taken care of, it'd be nice to see the custom layout stuff being looked at. But if everything else gets done except this I wouldn't be too upset.