While it was cool that we "built" our own lightsaber in KOTOR, it was pretty much "look at my guy move his hands and voila....a lightsaber."
I know this is a minor thing and if it didn't make it in I probably wouldn't care, but make it a bit more involved. Also....depending on how you could integrate it into the story, perhaps let you create your own double-bladed saber or an additional secondary saber. Sure...I could always just use one I found...but it just seems cooler using the one you created.
Perhaps, expanding on things a bit further, have the lightsaber you create a unique lightsaber, that is perhaps easier to modify (since you know the ins and outs of it). Little things like different hilts or stuff (although this is relatively minor).
Depending on what Jedi Class you are, allow some sort of uniqueness to it, perhaps even based on a character's intelligence (the neglected stat) or repair skill. This may make more sense with the prestige classes; maybe even make a limitation of a really good prestige class that you can only use a lightsaber you have created (but have the ability to modify better with your special abilities gained by your prestige class).
Like I said....not a big deal, but when I heard about the fact that I could create my own lightsaber, I was a little let down by it in KOTOR....maybe even just a little minigame