> Once you introduce connecting flights you introduce lost bags
Not necessarily. No connecting flights for pax with hold baggage (take the offer or leave it, MOL would love it)
> Flights can no longer be planned independently of each other
True. The schedules should be re-shaped anyway, even without any official connecting flights. Think of all these who change the planes "unofficially", think of millions of euros/pounds FR earns thanks to them. Creating more opportunities = winning more pax = earning more money
> it would definitely require a complete rethink of their whole business model
True. Why not earn more money using a mixed model. Fly cheaply combining flights on your own, say, 20 euros + 20 euros for a two-leg travel or buy a complete ticket (connecting flights) for 100 euros and lessen the risk. FR do not have to connect every flight everywhere. Just at one or two airports, just "safe" connections.
> FR's website can't cope with point to point bookings, how on earth will it be able to cope with connecting flights?
By selling the connecting flights via a different website or even outsourcing the service.