yet i wonder - what is the big difference. Is it "just" the new USBSerial chip? If so, what would be the big advantage above the 2009?
Basically - that, and the new name. From what I understand, it still uses the 328, along with a more streamlined bootloader (optiboot?) - I am not sure if this particular bootloader is smaller (the smallest you can have is 512 bytes), to allow for slightly larger programs to be loaded, or if it has just been optimized for faster upload speeds - or both...
As far as the new USB interface is concerned, you'll only likely see a "compatibility" issue if, for instance, someone changes or builds a project to change the firmware on the ATTiny (?) being used for the USB interface in such a way for the project, so as to change it to identify differently, or act in some other strange manner for the project so that a standard Arduino with an FTDI chip won't work.
I think though, that for regular usage (other than, again, faster upload speeds and possible bootloader sizes), the difference will be negligible.
I read that the UNO will now be the reference hardware - will that somehow make the 2009 obsolete or incompatible with upcoming builds?
Other than what I noted above, I doubt it. Think also of the large "installed base" of 2009 Ardunios - it is huge (for our market, of course); even if there were such an issue to arise, which I doubt, you would see attempts at "backporting". Likely one of the first things you'll see done, which might just be a "simple" re-burn - is putting the optiboot loader onto the 2009 Arduino (ie, the 328). You might also see interest in further "hacking" of the FTDI.
I honestly don't think there will be any "abandonment" going on (heck, they kept the same form-factor when they could've fixed the weird pin spacing - which, IMHO, they should have done - this was the one chance for a clean break, and for whatever reason, it was ignored). Also, note that the software still supports the really old-school DB9 serial ATMega8 Arduinos - which haven't been made in how long now?
If you have the money, I would take the time to look out for Arduino Duemilanove deals, as vendors move to bring the UNO into their lineup. I wouldn't worry about your current set of Arduinos being made obsolete or anything. This change is mostly about making the Arduino even more open (via the new USB chip - which we can now re-program - there's already a tutorial out on changing it!), and updating the "brand" so that it is easier for non-Italians to converse about the Arduino (Uno vs. Duemilanove).