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.
I would argue that if you're just starting out, grid hotkeys are more efficient since you can memorize either which key it is or where on the unit-card the button is located (visual cues tend to help memorization) - and if you don't know the hotkey, you can find it without mousing over the button.
Also, all the keys are on one side of the keyboard, meaning you won't have to move your hand as much.
That being said, the vast majority of players use the default keys either because
A) They don't know grid exists, or
B) They are already used to the default layout (grid was not an option in the beta), and/or were already used to the very similar layout of Starcraft 1; there really is no benefit to them learning a new layout if they already have the default hotkeys memorized. Most competitive players would fall into this category.
Best Answer
While I'm not sure as to what this problem was caused by, it seems to have been fixed as of Patch 1.1.