After trying to live with the original delivered Linux from Asus for a week, I've decided to reflash the whole thing and now it's running on Ubuntu Eee.
The stock system is too restrictive and way too many hacks to perform for someone who likes to peek under the hood. In the end, I get too bogged down by all the changes, multiple windows manager, and Asus Launcher (the simple interface you see on every Asus Eee PC) trying to be more than just a overlay program.
What I gave up is the option to go back to the original state (unless I have an external DVD drive) and the boot up time (super fast in the stock Eee 900). What I gain is the option for a better user interface and a simple way to upgrade application software (like OpenOffice, Firefox, Adobe Flash player, etc) without resorting to circus tricks.
Now I am happier with this new toy.