Playing the alternative gender will always result in some "differences" to the storyline.. but I highly suggest it. You can kick arse just as good as any "male", and the Carth romance has some truly funny dialogue options given the opportunity... :D
As far as mods go, it depends on what you like..
I've always been a Bastila fan, but when I play a female character, I'll be damned if she has a better wardrobe than me (2 snaps in a Z formation.. uhh) hehehe.. :lol:
I prefer RedHawke's Bastila's Clothes For Female PC's (
http://www.pcgamemods.com/mod/7833.html)
or (shameless plug) mine and RH's ;) Xia Terashai Set (
http://www.pcgamemods.com/mod/10220.html) (limited to Asian female PC's because of skin tone)...
JdNoa's Alternate DS Dialogue (
http://www.pcgamemods.com/mod/5326.html) is a good one to, (but it's more of a DS mod).
KristyKistic just released the Meet Athena (
http://www.pcgamemods.com/mod/16987.html) mod recently.. and it looks like a great one to choose as well :)
If all else fails, try a "search by mod name" and use key words such "female" to get a decent listing of mods....