Joomla 1.6 breaks a lot of existing 1.5 extensions apparently. I think the official extension site will therefore have three compatibility graphics on extension listing -
1. Joomla 1.0 Native
2. Joomla 1.5 (Native or Legacy)
3. Joomla 1.6 (Native or Legacy)
...i'm just guessing though, I don't hang around the official J! forums too much. All I know is that J! v1.6 has the new version of MooTools (1.22 or 1.3 or something) which is not backwards compatible with current J1.5 MooTools, so quite a few extensions and templates will have to be edited/hacked/re-written to work with the new Joomla.
BTW, how good is the new in-built Commenting system anyway? Is it more powerful than JoomlaComment? That would be sad