Well, look at it this way: A mini's pretty much an automatic conversation piece, since a person has at least a chance of having seen a bartop before. But a fullblown mini is pretty much the realm of the homemade rig, aside from a few exceptions.
Of course, things also depend on how mini you want to go. A 4' mini set up at an angle so that you can pull it over to the couch and play it perfectly with friends or whatnot is a highly different beast than a 2' mini you practically have to lie on the floor to play, for instance.
A bartop will run into similar, though distinctly different, problems, of course. Your average design just does not work without being on a table or counter of decent height, which limits where you can put it. On the other hand, you can also make your bartop wider than your mini without it starting to look funky, which might be nice for 2-player setups.
Me, I'd go with the mini. But I also didn't grow up in the '80s, and thus have no major urge to perfectly recreate a more classic arcade machine design. If you're more of a stickler for having a machine that DOES look like it could've stepped out of your childhood/young adulthood nostalgia, the bartop might be a better choice.