Yes, I'm afraid skins and mods made for 2.x will not work in 3.x. The changes are just too big to accommodate older work.
For instance, the template system supports "plugins" which we heavily use to apply display related tweaks to data in the template rather than in the source files. This makes customizing how things work much much easier (think of things like formatting dates, or numbers (1000 to 1,000) and so on). We're combining multiple templates into one so that when you want to edit the topic view page, you edit the page, not the 20 templates that make up the page. There's a ton more changes coming on that front, which we will blog about in the future.
However, it is safe to assume that given these changes skins can't possibly work in 3.x. It will take a little time for skinners and modders to update their code (and we will be providing helpful guides near 3.0's release), but hopefully moving forward things should be much much easier for everyone involved.