Unicomp's key cap quality has varied over the years, which is probably why the OP has a mixed impression. For a time, their caps had an excessive amount of flashing around the bottom. This comes from overusing a worn-out mold. They seem to be better now. The ones I got a month or two ago are no better or worse than stock IBM caps.
Their custom printing process was previously done by hand using original equipment, so the alignment tended to be all over the place. Even the standard legends tended to drift around from set to set, probably due to worn-out equipment. They have recently purchased new dye-sub equipment and can not only do custom legends, but they can also do more colors. Before they made this investment, they could not do things like this:
http://pckeyboard.com/page/category/SBLEUnicomp tends to move slowly, but they eventually do get there. They recently refreshed their entire line of keyboards, seemingly to reduce the number of part variations that they have to stock. While some of the things they did with the new layouts are not the greatest, it shows that they are actively trying to keep their product line going. Hopefully we'll see some movement on the custom key cap front fairly soon.