I suspect your premise about gaining more points for winning than losing is slightly off. Generally speaking, once your point level stabilizes due to finding your actual skill level, your points will remain the same relative to others playing the game if you don't get any better/worse.
However, the total number of points everyone has will trend upward due to the Bonus Pool. This does mean it rewards playing more often, but only to a certain extent in a certain time period (a few games per week, I suspect). Once you've exhausted your bonus pool, your ranking points will again more-or-less stabilize based on your skill.
One of the reasons this was done was to encourage people to actually play the game. Since everyone's points are constantly going up, you have to play to keep up with your peers. If this artificial inflation of points due to the bonus pool wasn't in place, the player at the very top would - in theory - not have much reason to play; he's the best and his points will stay the highest until someone usurps him. This way, he has to keep playing to maintain his status. As with any fair matchmaking system, the more people playing, the better, and I think Blizzard is trying to encourage more people to play.
However, none of this is cut and dry so there's no one reason for any of these decisions; likewise it's not at all obvious whether this system is superior to the traditional ranking system you mention.
That said, here are some good articles on the subject:
Note also that the points you see displayed and used for your ranking may be separate from the underlying statistic used for matching you up against other players. The two stats should converge on relatively the same thing, but the Bonus Pool adds the extra incentive to play more often.
The short answer is: Points are not Comparable across leagues.
The accumulation of points is supposed to be proportional to the difference in skill between players. Unfortunately, the points you gain are unrelated to your ELO style rank. Because of things like: Bonus points, starting off at 0 points, and league promotion devaluing points, points don't correspond to a true ranking.
Instead, sites like SC2Rankings and Starcraft.org realize that the hidden ELO style rank that Blizzard uses is only accurately reflected in promotion between leagues. As a result, the best indicator of skill is what league a player is in. Since points are comparable inside of a league, the secondary sort these sites often use is that point metric (despite its deep flaws).
I'll probably write a longer explanation of how an ELO style ranking system should work to highlight why points don't, but the bottom line is still going to be: points aren't comparable between leagues.
Best Answer
Ive played through a couple promotions and it seems like points are maintained across promotions.
I know this wasn't always true, but it was on nov 17 (last promotion I had).
That said there is no good way to compare players who haven't faced off... Period.
Not across leagues, not across divisions, not within divisions. Points are a completely inaccurate measurement and rankings are based off of points. If we look at the blizzard top 200 (released) we see poor correlation with points. Blizzard uses hidden ranking for those numbers. If we compare that ranking to the ELO ranking that some fan sites use, we see an even different set of results.
The reality is that voting systems (game theory) require impractical amounts of data for a game like starcraft. The result being that you rarely ever get an accurate ranking system.