Well Darwyn, I've discussed what you're talking about for quite some time. It's not that the points system isn't representative of skill, because it very much is, just as an average over a length of time. joao losing his 1000 pt game is quite likely as he'd be playing against players of a 1000 bet calibre. However, he'd likely rise up again to reflect his skill. If you look at the Hall of Fame, the ranking is very similar to win ratio. The points system encourages a high win ratio as well as prioritizing higher staked games. If you look, the top 10 all have around 40% win percentage, the top 30 have around 30% win percentage etc. There are a few anomalies, but none that are gamebreaking.
However, there is a problem with the points system that The Ghostmaker has shown me, but that problem is inherent in any win ratio system as well, so your secondary one would not resolve it.
The problem with the points system is as follows. Theoretically, if you played players who were exactly your skill level at the same pot level, than over time your points should remain fairly static as you win and lose in equal ratios to people of your own skill level. However, if you consistently play stronger players, you might win some, but you will mostly lose them as you are the weaker player. So on average your points will continue to decline, despite that your skill may not have declined, in fact it is probably better for playing the stronger players. In a similar fashion, if you consistently play weaker players, you might lose some, but you will win more ratio-wise as you are the stronger player. As a result your points will slowly climb despite that your skill may not be increasing at the same rate. As such, the player who plays stronger players has a lower rating than the person who plays players of a similar skill level who in turn has a lower rating than the person who consistently plays weaker players.
The same problem is inherent within any ranking system relying solely or mostly upon a simple win ratio. As playing weaker players guarantees a higher win ratio, and playing stronger players guarantees a lower win ratio. Of course this problem is purely theoretical, but we can see some of the effects as players who consistently play against stronger players are pushed to the ground.
I wouldn't overhaul the points system without a flawless system coming in, as this is it's only flaw that I can see, and despite that flaw we have a fairly decent Hall of Fame.
I'm interested in what results The Ghostmaker's proposed system will have now that he has the database. I'm not quite sure it's flawless system yet, but it certainly addresses the problem that the point system has, though it'll have to replace the point system in all roles before it replaces it.
I don't pretend that this discussion will actually lead to any change, but I hope the debate leads to some ideas. I don't want to incite any dissatisfaction with the points system either, as it is a very good system. Extremely impressive, and I think quite the step up from the simple win ratio system that was advocated by me prior to the point system.