The newer one just looks cheap to me, like some kind of Happy Meal toy. I know it reuses the BAD parts and easily comes apart so maybe that's why. Honestly I bet we get a "redone" R5-D4 in a few years since they redid the R2-D2 mold (and it's a fine mold, IMO, although I would like to see some slight mods for a "normal" rerelease).
But yeah, I'm sticking with the 2006 version.