I would have to say, go with a REMAP.

The stock ECU is fairly powerful and has an excellent closed loop operation to maintain fuel economy. Injector sizing is also not much of a worry as stock ecu's support Injector Scaling which means you can run any size injectors you want. Boost Control, Ignition control, Fuel Control what more could you ask for

If you are worried about CEL's etc , you can selectively disable the code

IE

P2040 - Cat Inefficency can be disabled by a "05 00 00" code

Leaving you with all other ODBII codes intact.

Motec, Link, Autronic are all fairly good aftermarket ECU's (each has their own merits and i wont startup the whole motec, autronic, link flame war). If you were to run advanced features such as Antilag, Launch control blah blah.. i would then say go for an aftermarket ecu.

Ahh yes.. as for link offering better economy over a motec.

Get your tuner to recheck his/her tune, maybe something is up with your engine.