Main thing I'd like them to add is some hair styles that don't look like molded-rubber wigs. Having all my characters bald because I can't stand the way they did the hair is hampering my enjoyment of the game!
Also, for Klingons - they need to fix all the clipping problems with what they before they add more costumes. And boots... how about some that don't look like Herman Munster apparel?
Borg attachments? Are there borg BOs other than the pre-order special? Since I'm not a pre-order customer, I'd object to them spending more time on features that only a few of their customers can make use of. It's bad enough that they shipped the game with so much exclusive content in the first place.
I'm sure it's been said, but Enterprise-era jumpsuits would be nice, and I'd also like for a standard uniform option for my crew, not just BOs. It's kind of weird to see part of my crew in the grey-on-black uniforms, and the other part in the 2409/STXI-looking uniforms.
Believe someone told me this is already in the pipeline but wanted to state it anyway. I'd just like to see any uniform we have access to be able to be worn by our BOs too. But, again, think it is being worked on.