There are definitely times when you want the "older" version, and not have your Build Queue touched.
Tade Centers vs Banks, and Research Academies vs Neutrality Learning Centers are classic cases. The lower-tech versions are FAR faster to build, and you get the (substantial) benefits much earlier.
I'd often build a bunch of Trade Centers, then wait to upgrade them to Stock Exchanges, and forgo Banks entirely, because they (banks) were simply too expensive in terms of build time (70 for a TC, 120 for a SE, and 200(!) for a Bank?). In the case of the NLC, I'd ALWAYS build a Research Academy first, then, after it was complete, upgrade it to a NLC.
Overall, I wish there would be a button on each Planet screen that is labled "UPGRADE!", which would then auto-upgrade all buildings in the queue to their newest version, PLUS add to the queue the proper upgrades for existing structures.
Otherwise, I'm NOT a fan of auto-upgrades.