how long have they had a fuel surcharge ?
Jet2 imposed Fuel Surcharges on mid-haul flights from the date that Summer 11 flights went on sale last August. Fuel Surcharges were added to short-haul flights around December. I booked flights to Faro in November and there were no Fuel Surcharges then. If they know that far in advance that a fuel surcharge is necessary, I think it should be incorporated into the basic fare.
There's also an on line check in fee which seems impossible to avoid.
Correct, you are in fact being charged for printing your own Boarding Pass.
Neither of these is obvious until the very last stage of the booking
Again correct. It is a case of watch the price escallate as you progress through the booking process. Hopefully some watchdog will put an end to this deviousness and make these airlines show a total price up front for all non-optional charges.