Awakened Undead and Ability Scores

Here's the scenario, as it stands:
I'm approching the level at which I can begin to cast Awaken Undead. I have, up until now had a host of various monster skeletons. What I would like to do, in order to fill up my HD limit is to have a few Awakened undead lieutenants with class levels, rather than a skeletal horde. I would like to give them levels in some low tier classes that have caught my eye, that way I can play those and not outshine the rest of my party. My particular preferences are Ninja and Warlock (no PrCs or anything else, just those classes).

The main barrier to doing this is that for flavor reasons I would like to make them Human Skeletons and those tend to be worse than various monsters because of the lack of Ex abilities. My DM won't allow me to roll ability scores for them, in spite of the fact that monsters I can get by RAW would be more powerful.

So I would like to find a way to give the skeletons better WIS or CHA scores in a way that exists within WotC published material.

Thank you.

You can increase stats by up to 5 points through tomes or wishes, but this is a very, very expensive way to go.

Have you thought about making some human followers into Necropolitans if your DM will allow that? Not that ninja skeletons wouldn't be cool...

I have actually been doing some research of other possibilities.
In another forum the suggestion was "forget it and just make ghasts." This was my original backup plan.

I did, in fact, come across the Necropolitan follower trick, but that would require me to learn the ritual and get other people to participate in it. Trust me, my DM would care about this.

I think that I'm approaching this the wrong way. My real question should be what is the point of Awaken Undead except to get skeletal/zombie monsters with their Ex abilities? What I am attempting to do is create an undead version of an awakened animal companion that takes on a character class. The thing is, the Awaken spell gives the creature 3d6 Int.