I think everybody in this thread had some great ideas, so I made a mish-mash of everybody's ideas.
I took the idea from xfin where stat points added at character creation wouldn't be wasted (or exploited by removing them).
Then I added maey's idea of summing the total skill then taking the square-root to figure the bonus stats. I thought that was a bit too easy to get the first couple points (at 1 and 4 skill) so I changed those to 2 and 5 points, then the rest at 9, 16, 25, etc. All skills at 10 will get you 8 bonus points.
Then I added my own flair by only counting skills if they had at least two points. So if you have 3+2+1, it'll only count as 5 total, but if you have 2+2+2, it'll count as 6 total. I also cleaned up the code a bit and restored the "updating stats" messages.
I considered adding some logic in to make it harder to get bonus stats if you add a bunch at character creation, and easier if you remove some. I haven't figured out a good equation though, so I figured I'd leave it and test it like it is.
I can add a download link to my changes if anybody is interested.