One interesting difference is that N900 is the main product, while Android Developer Phone is just that, a side product. In general one cannot select any Android phone from the market because of the limitations, instead having to trust there will be sensible... no, even cool dev phones from Google.
In my mind I also prefer N900 simply because its developers did not decide to throw everything on top of Linux kernel away, and have greatly contributed to GStreamer, D-Bus, now Qt, etc. over the years. Android seems more like Symbian in the sense that it was (or is) vaporware and then BOOM, there is a code drop of open source code but no open source community. I simply don't like all these proprietary vendors doing code-drops and then claiming they are open source right away - there's much more to open source than the code, and it takes years to build that.
/me uses Neo FreeRunner until there is some other phone fully usable with Debian, so therefore I'm interested if it takes a year or two for eg. N900 to be fully usable with Debian.