I just recently upgraded to CS6 from CS3. I printed the exact same file in CS3 (Same color space, same bit depth, using the same profile and rendering intent and same ink laydown) and then printed that file in CS6 - and they turned out vastly different. What variable am I missing here?
We cannot know. You're not telling us what profiles you actually use, what printer and whatnot. And yes, the printing stuff has changed, profiles have been updated, so some adjustments are necessary no matter what.
Check carefully the settings in your print dialog, specifically the color-management settings. Also check your printer settings to ensure they're compatible with the color-management settings you chose in Photoshop.
Put some screen grabs up and describe your settings (ideally from both versions), and maybe someone will spot what's up.
There's always the possibility there's a printer driver problem being exposed by the new version. It does use different printing APIs on some systems.
P.S., Good morning, Mylenium. You're up early.