bevinator: BFG is on id tech 5, whereas the original was id tech 4. That's why mod compatibility is broken. Currently, however, id tech 5 is still Zenimax's in-house engine, so modding on it is understandably extremely limited.
Personally my anger over the issue isn't "I wanted Doom 3 but I can't get it anymore," but rather "Horey sheet these guys are the greediest fuckers on the planet!"
Why? Really, honestly, do you think they're twirling their mustaches because they actually thought there was a horde of people lined up to buy classic Doom 3, inexplicably after D3 BFG released and they think they've forced them to all pony up much, much more (instead of waiting to get it for like 5 dollars during Christmas, call me Nostradamus when it happens)?
I really think it's much, much simpler than that:
1) Supporting a single version, the version of the game most of the developers know best, on the platform they know best, which is newer and probably has an easier to work with toolset.
2) Reduce consumer confusion.
I really think people are jumping to an illogical conclusion on this one... If people hadn't paid 3-6 bucks for Doom 3 yet there's no way in hell they're going to suddenly pay 40 dollars for the "super-duper" version. BethSoft and id both know that.