I agree with ajamieson - if anyone decided to offer a lo-cost alternative Czech airlines would surely get nailed!
Scotland-PRG is surely primarily of a leisure route? There isn't a major opportunity for connections at PRG is there?
Seeing as Ryanair don't yet operate to the Czech Rep. I would have thought RYR PIK-PRG might be a while away. Bmibaby might be the most likely if their new base were to come north.
There's always easy/Go - they did apply for EDI/GLA-PRG a while ago but presumably their diffs. with BAA precluded it?