Ultimately - and we're talking a good ten years down the road - the availability of a third runway and sixth terminal at LHR will allow BA to increase some of its s/h routes there, so I would expect that by then, BA will have a very limited presence at LGW. I'm assuming the whole O/S issue will be sorted out by then (not necessarily a foregone conclusion!).
What happens then at LGW, as far as Flybe is concerned; it only operates three LGW routes - GCI, JER and BHD. Will it expand into some old BA markets, or will U2 be moving quickly to take up most of this slack. And of course, one can't rule out FR taking full advantage of BA's departure.