I think many of us saw trouble on the horizon when the States of Guernsey decided to take control on Aurigny. Just like most state-run airlines, it has struggled financially. Only the airlines which are run as a true business generally prosper.
I know that the States of Guernsey had the Channel Islands best interests at heart when they decided to move in for Aurigny in 2003, but the airline has become too fragmented to make any money.
The inter-island ops are vital and should be the priority. Flybe have cried time and again their commitment to GCI and are in a much stronger position to evaluate new services from GCI than GR were. LGW will always be served by BE so there is no need for GR to fly the route if they aren't making money on it. BE would also no doubt move in to serve MAN if GR didn't make money on the route either.
As has been mentioned before, there are too many aircraft types being operated too. I agree that the Trislanders should operate a high frequency GCI-JER service as well as the other island hops and perhaps 3 ATR42/72's would be sufficient for LGW/MAN services if these routes do actually make money for GR. I think the Saabs are on the way out anyway and so the third (backup) ATR could operate any peak GCI-JER flights which the Trislanders were too small for to also enable the Shorts 360's to be sold.