Its the airlines, not JY that determine which airports they use for they're fleet. In an ideal world there would be flights from your regional airport to anywhere in the globe, but with larger aircraft and more destinations to choose from only the larger airports would only be able to accommodate these routes. Many airlines would not even consider flying from anywhere in the UK other than London Heathrow or Gatwick. If there was a flight from Glasgow to Malta or Mongolia JY would try to shoehorn a tour in somehow.
If been on guided trips to Europe where there are two days in the week designated to hotel/airport transfers (Saturday & Wednesday). This was to accommodate for flights coming from various UK airports that may be once a week (or for Gatwick both days). So halfway through trip half of the people left and replaced with newbies. So it was flexible enough to fit in more than one place of origin and you could have 4,7,10 or 14 day holidays. Whilst this wouldn't be feasible for tours of Peru, China or Kenya or cruises, it could be for destinations in Europe and 'Escape' holidays.
From my perspective I have very little sympathy for those complaining about a 2-3 hour coach or train journey to get in to London. Sorry. I live in Jersey, so every holiday outside the UK entails a trip via Gatwick, 99% of the time it includes an overnight stay on either before the outbound or after inbound flights or sometimes both. No matter what company I use this has to be the case and adds at least £300 to the holiday regardless of its length, if I book nine months in advance. I don't do last minute breaks as this can be in access of £700 easily, no matter what the 'deal' is on offer.
I've already booked two trips next year with JY. Basque Country of Spain at the end of April, and Sicily in September. I've recently returned from Sardinia (loved it) and I booked the Spain trip back in June, so I could get cheaper Jersey-Gatwick flights, find a hotel at Heathrow and work out how to get between the two airports. And I am considering my first long-haul in 2018 (early 2018 dates?)