Well I had a very quick look and the fares don't seem to have sky rocketed... it's possible to book a day return in three weeks time for less than £160 all in (via AF site) which is not unreasonable. If the fares do get crazy, then no doubt a third airline will see an opportunity to win some passengers by offering lower fares.
Flybe aren't really a "no-frills" airline - they have rather successfully placed themselves as an inbetween, neither full service nor no-frills, niche airline. They offer lounge access, a frequent flyer program, flexible tickets, interlining/connections and allocated seating etc. The only real difference between AF and BE is that there is no complimentary refreshments on board and there may be a charge for a checked in baggage.
However, it the responsibility of AF to inform passengers booking with them that the flight will be operated by BE and make them aware of the differences. Looking at AF's website it is not specific about meals (says meal info not available) and it says there is a 1 piece/23kg checked bag allowance with no mention of any charges. Of course, it may be that pax booked through AF will be provided with a meal voucher for use on board and a complimentary checked bag... I am sure this will have been considered by those involved in working these things out (at least I would hope so!).
As for the Q400... I agree everyone is entitled to their opinion and I have heard people moan about the Q400, but likewise I have heard many positive comments also...
Granted, it can be a little noisier than a jet depending on where in the cabin you sit and how well the NVS system is working (if not working correctly it is sometimes switched off until it is fixed).
As for the flight time, the difference is pretty insignificant. The block time from MAN to CDG is only 5 or 10 mins longer on the Q400 than the E195 and if a flight leaves on time it will often arrive on stand early at CDG (the schedule includes padding for slots etc.).
And remote stands - I cannot comment on whether this will be the case at T2 at CDG but while BE have been using T1, they do not park remotely and it is a short 20 second walk into the terminal building (except on the odd occasion where the aircraft has been parked at a satellite which is closed for refurb in which case a coach is needed - not the fault of the Q400).
Oh and large bags - those lockers are deceptively large and most trolly bags that aren't packed to bursting point will fit although the narrow opening can make it interesting trying to get the wheels in! But if they don't fit in the locker they will fit under the seat in front - and if they don't fit there, then they should never have made it into the cabin in the first place. Unfortunately, many passengers don't think that the cabin size requirements apply to them and their beloved bag and then complain when they get on board can't find a home for their bag
Oh and by the way, I am not a Q400 pilot
