I don't know if this has been mentioned already here but...
There are apparently large blocks of code in MOO3 which were written by people no longer with the MOO3 Team, and the remaining people don't understand or know how to make heads or tails of these blocks of code to fix any problems which may be hiding in there
The general feeling comming out of Atari is that they aren't going to support MOO3 anymore then they already have. People are now clinging to the great white hope that could be MOO4. Atari isn't in any great hurry for another MOO game though...