First comes the superficial aspect. Sex, face and voice of the character.
Adjusting the facial features you won't have the same freedom as pretty much every RPG out there today has, where each and every facial feature can be adjusted, which in a long run leads to every character in the game looking a bit off and on some level exactly identical to each other because they all are based on that very same model that have been modified just a little bit. 2D drawings would have the advantage of originality and variability, but is a lot more burdensome road to travel.
Instead I'm thinking of combining those two. There would be series of stylized meshes for the player to choose from for the head shape. Eyes and mouth would be sort of animated textures on the mesh. I loved how they did the facial animation in Grim Fandango so that's the style I'd like to try out.
The character's skill creation sequence is like a job application. The player fills out the forms and decides what kind of character he will play. Where they come from, how old they are, what kind of training they've had, all kinds of personal information that some won't even have much to do with the game itself.
After this the player is given a certain amount of skill points which he can deploy any way he wants. These points determine the character's talent in various skills and attributes which will be needed during the game.
After filling out the basic forms the player will decide the specialization of the character. Two can be selected from a long list of different military skill sets, which will give a hefty bonus to skills involved in that area of expertise. This decision has a lot to do with the course of the coming game because different specialists fight a different battle. So if you decide to be medic, you won't be sniping headshots while sitting in a tree any time soon.
Skill points won't be earned after the initial character creation. Instead you will improve the skills by practising them. For example by shooting, you become a better shooter, you won't earn points from it which could be deployed in another skill like stealth. So a medic can become a sniper only if he practices with a sniper rifle.
As you can imagine you won't be able to create a super soldier who is a master in every aspect of the game right at the beginning. Instead you can (or it is recommended to) concentrate on few selected skills so your character won't be mediocre at everything but lousy at some skills but promising in others.
This is the recommended way because you're not fighting a one man war. You can hire up to twenty other characters to your aid whose expertise will compensate your character's lower skills.

These characters can be professional mercenaries from every aspect of warfare or volunteer freedom fighters who will be willing to join the fight as the game progresses. They are much cheaper to hire than the expert mercenaries, but this shows in their lack of skills.