If the entire decision-making managerial power is 100% Allegiant management, a lot will depend on whether they are willing to pay what it costs to succeed with respect to moving to a single cert and opspecs. It will probably cost more than expected, and present a lot of challenges that are not visible yet (as alluded to by Nibake).

I know nothing about the acquiring airline's management, but knowing about how things go in this industry it is often really hard to get the money guys to put out the needed cash for a durable, quality solution. Adding to that, any unrealistic deadlines from top management can cause long-term consequences. You'll have a fleet manager or chief pilot saying "we really need solution XYZ", and the word from on high is "make do with the cheaper faster solution".

Another question is the FSDO / CMO that will have jurisdiction, which I assume will be Vegas. Does MSP have to agree with any short-term solutions during the shift to single-carrier? What roadblocks await?

Given that this move is toward growing into a much larger airline, hopefully there is some willingness on your management's part to invest where needed to ensure long-term operational success.

This is the benefit of a fully unified group of 2000+ pilots - we can speak with one voice for those issues, especially where it takes a line pilot's perspective to overcome/influence management's cost-saving impulses and exuberance. Ask me how I know...