What difference does it make?
Even if there was no 'express pilot' and 'mainline pilot' classification, you'd still have the payscale differences. If US mainline had never had express operators(Mesa, Allegheny, etc.) and assumed those operations themselves, how would things be any different? You'd still have the furloughs, you'd still have pilots being 'demoted' from Boeings and Airbuses down to EMBs and CRJs.
The express carriers are paying what they can afford, given the pricing power (or lack thereof) that their partner airlines have. To see them start flying 90 seat aircraft is unprecedented, but yet another reality of the market. I doubt we'll see those EMB190's going into small markets like LNS, MDT, DUJ, etc. though. I'm thinking they'll be more of the medium cities like IND, GSO, RDU, etc. This is where the F100s and 732s flew at one point or another.