Here's My Take
Very early in the game it should be determined which side is assumed for the first 2 games. Also I like the idea of the PC being a young Jedi from a peaceful planet on Curascant. I would like to see a young PC with no history or baggage. And he/she has a Jedi master who is young, after all the Jedi are still rebuilding, but the PC becomes a Jedi Knight near the middle of the game. Also the rudimentary universal Force Powers: Speed, Lightsaber Throw, Push, etc. should be with the PC at Level 1.
Characters (Light Side)
Bastila (Jedi Council)
Handmaiden (Jedi Council)
Disciple (Jedi Council)
Bao-Dur (Jedi Council)
Atton Rand (Jedi Council)
Mira (Jedi Council)
Jolee Bindo (Jedi Council - though not really calling himself a Jedi this reclusive old coot has returned to train a few people and do his part to get the galaxy back in order. Despite his misgivings about the Jedi code he knows the Republic needs Jedi to maintain peace and order)
NPCs - I would like to see mostly new NPCs and the ability to chose some NPCs, but not all, with no relevancy to alignment or gender
T3 and HK (gotta work in the droids somehow
Wookie with Zalbaar's power and kind, honorable spirit, like Chewie but with Hanharr's rage ability
Female Mon Calamarian Jedi (not master though)
Human Jedi Knight who serves as teacher to the PC
Adept Jedi human who is the PCs love interest with a love story that actually sees some development, similar to the PC and Bastila in KOTOR
Planets/Moons (in no particular order but I think the important planet that's the finale of the game should be made up)
Coruscant - planet the game starts on
Corellia
Mon Calamiri
Kessel
Yavin 4
Carida
Onderon
Utapau
Tatooine
Bespin
and Def not Korriban or Dantooine (I liked both but they have been played out)
Other things I want to see
Customizable PC
Customizable Lightsaber hilts
Customizable robes and robes that offer more amenities and as much defense protection as medium armor
More emphasis on characters who specialize in blasters and more emphasis on battling with blasters altogether (in short just make blasters more awesome)
PC gets lightsaber almost immediately
Less, or (please Lord) no bugs
A plot and story that has resolution at the end (in Kotor II i was left thinking, what the crap? and for the final cutscene at the end, i was like, well what the crap does my character do now?)
Side quests based on characters - such as getting Carth to talk about his wife and son in the first game or Jolee talking about his life before meeting Revan and side quests that deal with stuff about the NPCs such as Jagi's Challenge and Batsila's Mother while still having the power to influence characters as in the 2nd game
When u become a Sith NPCs should show you proper respect and when a characters alignment changes they should change as well (I didn't like turning Handmaiden all the way to the dark side so that she got bonus points for strength and she balked when I killed a character because i wanted to)
More powerful final villian and a quest that shows you what you are doing and why you are going to that planet (i. e. what you're goal is on Malachor. Of course you know you were there to confront Sion and Trayus but I still like to see it in writing)
I think the last thing I want is a good engaging plot that keeps you guessing what's gonna happen to the PC that you have become so enamored with you can't wait to get home from work and live his/her life.