well, i had to ask myself that question a few weeks ago, and i decided on 2009WBE.
I dont, lets say, regret it, but you should know there is not much you can do with it at the moment. Yes, you have all the earlier content, but most of it has problems (the often mentioned alpha channel bug and others).
You will spend a lot of time sorting out content that works and that "somehow works", making content yourself got much harder if you are not used to the new stuff (normal maps and such).
If you just want to work with existing routes and content, i would say you should go with an older version and safe yourself time and trouble. Nearly everything you ever download from the DLS is compatible with 2006.
If you want to build routes/content, counting in how much time it usually takes to build anything, i would go with 2009, because the 5m grid is really nice for routes, and the grafics wont want you to go back, ever. Yes, you spent a lot of time to learn the new stuff, but the quality will be higher then ever before.
Just my opinion