First off, can someone point me toward the rule that says you can't play 3D objects unless your opponent agrees?

And second, I've heard that that's changed now, that you simply choose three tokens and replace the light objects with 3D light objects, or the heavy with 3D heavy. Can someone tell what's changed?

To tell the truth, I'm not sure why we do things the way we do at my venues, I'm guessing its more house rules than anything. From what I've read, each player simply brings three objects, and it sounds like now you can just choose three 3D objects and place them if you want. But my venues have always placed 6 object tokens face down, and each player picks three and places them.

So can someone point me towards the truth?

Actually...3D objects are always legal now. On wizkids site, look for "Rules for all WizKids Games", then in the HeroClix section. That is the best place to find all of the current rules.