My first choice was a direct upgrade, but I made some mistakes in managing the 2.9.2 instance that need to be wiped clean and started over.
Plus our environment is a shared one with other enterprise groups, which meant that someone else was managing our OS patch upgrades. After our WPMU server completely failed during one of those upgrades, we decided to split the shared environment into Dev and Prod systems so that OS patches could be tested on Dev to make sure they didn't kill WordPress. Since the Dev environment didn't exist prior, and the network tech didn't have the time to replicate WPMU 2.9.2 on it so we could attempt a direct upgrade (only enough time to drop 3.0 on it), we had to opt for the fresh install and migration.
See, told ya' it was complicated. LOL
I'll take your word that the database structure is the same. But one item I neglected to include (sorry) was the fact that we're changing the table prefix on the 3.0 instance for security purposes and so that it matches what will be our not-yet-installed 3.0 Production instance so we can easily script a mirroring of the data between the Dev and Prod environments.
Will we be able to globally find/replace the table prefix in the exported SQL statements before importing the WPMU database to 3.0 and not experience trouble? Any exceptions to that find/replace that you know of?