Electronicobby1,
have you checked what the Arduino platform is built? It's a bunch of open source components doing the heavy lifting, glued together by a mediocre GUI in Java and a boot-loader for the ATmega plus a few libraries of variable quality. Some are useful, other aren't much more than code fragments copied from the Atmel data sheet.
So where can this vendor lock-in based on the USB-ID you're so afraid of can come from? From the boot loader? From the GUI? From the third party open source AVR-dude library? For all except the GUI, that problem will be patched out faster than you can voice a complaint. If they decide to mess with the GUI, you can bet on that it will be replaced quickly, perhaps even an eclipse integration. The GUI doesn't have much unique functions, it's just a nice to have application which survives because it doesn't offend and creates no hassles.
All in all, I think your fears are totally unfounded and the development we see here is very positive.
Korman