I love Eve Online and seeing the ABP reloaded that also look great to let the players make their ideal hero. For me seeing my original hero on screen makes the story that more engaging I can actually forgive shortfalls because its my hero in the scene but it also makes the best moments more full filling. For me the more realistic I can make my hero with a touch of fantasy the better.
Customization engines I liked
Eve Online - as many have said a wonderful engine too bad they waste this by placing you on a ship all day I can't wrap my head around this give a great engine and have you sit in a lobby all day.
APB - looks just as great as EVE but has some more abilities like making your own tatoos and placing them how you want on the body and clothing. Making your clothing from scratch, specifically toning or tearing your clothing as you see fit.
Mass Effect 1 - This is on the other scale a pre determined body but custom head decent options and tweaking of faical features is very nice
KoA: The reckoning - similar to ME but more fantasy based it was again custom head on pre-determined body but the choices where less realistic and more fun.
Dragons Dogma - This is in the middle players can choose from several pre determined body types with models shown in their clothing so players can quickly tell just what they're getting, unique selective hair styles, they do allow for some basic tweaking of color, eyes, and lips to name a few the system was well done for a middle ground system in the end you could mix any hair, eye, with any body type and make very unique characters.
I'd prefer the most freedom possible like EVE but mixing the systems could also make for an customization system worth exploring. Whatever system they use would be determined by how sandbox vs predetermined the story is.
I agree with other poster who state they'd also like a customization system for their cybernetic parts. I would like to go EVE body detailing to decide what parts go where and what do they look like what I mean by look like is I could decide do I get parts that look like Adam Jensen's all sleek and deathly or do I get parts that look like the bling drug dealers in the same game their parts are gold, low grade, but still hold an appeal visually or would they be flesh based like Kusanagi's where its indistinguishable from human until revealed otherwise. Changing the add ons colors or the tone of the whole say arm would be neat too. This menu can be reaccessed at