if you go tile, you need a good sub surface that will account for the expansion/contraction. other wise the tile will just crack. the shows always use some orange stuff they roll out then put the tile on it.

you can use concrete patch to fill the joints, but don't think for a minute that it will never crack. usually after the first year it has let go.

That orange stuff is Schluter's Ditra - we used it in our bathroom.

I've seen stained concrete floors in stores where they've filled the expansion joints with something before they applied the stain. It almost looks like a grout joint. Any idea what I could use to do that?

maybe a concrete caulk would work, at least it would be forgiving to some extents.