There is no seperate Shuttle per se... It was once a wholly owned subsidiary (Shuttle Inc) but was merged into the mainline in 2000. At one point, (late 90s?) mainline was doing Shuttle service with DC9s to IAD, with Shuttle titles, but mainline planes and crews, while the "real Shuttle" did the standard LGA BOS DCA.
The gates/slots can be used for anything if sold, as long as they are within the perimeters for LGA and DCA. It could still easily be sold as a package deal, the slots and the Shuttle specific gates, lounges, and ticket counters.
The company did have a dedicated Shuttle fleet of A319s and A320s after the Shuttle 727s were phased out. They were single class, with lots of legroom like the 170, and I can't remember but I want to say the gallies had no ovens. Siegel decided to have a standard fleet, so the planes were reconfigured and regular dual class Airbuses (and I think 737s as well) now fly the Shuttle routes. The aircraft don't have the Shuttle titles, but the brand is still widely used in gate areas and marketing, and the flights have Shuttle flight numbers (I think they start with 2). As far as announcements, onboard service, and airport procedures the Shuttle brand is still used, albeit on dual class "mainline" planes. There is no division for crews, they now do both mainline and Shuttle flying if based in LGA DCA or BOS.
The difference between Shuttle and MidAtlantic is that it was a wholly owned, seperate certificate airline, like PSA or Piedmont, which MidAtlantic never was (although there was Potomac Air, the defunct W/O that was to become DCAir, and later MAA, but never did, but that's a different story). MAA is more similar to MetroJet in that it's mainline certificate but different contracts for pilots (but not F/As as well like MAA). Of course. MetroJet was a public brand, whereas MAA wears US Airways Express titles despite the fact that it uses the mainline brand (flight numbers, website/boarding passes, meals etc).
As we all know, US Airways is determined to be as confusing as possible for it's customers and employees.
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I miss the chic Shuttle planes, as well the foxy red MetroJets.