Ive run plenty with LINK ecu. I run the drive by wire either the 1uz VVti with the accelerator position on the throttle body or the 3uz with the external pedal assembly. With full cam control we generally head for around 220rwkw on a stock engine. On the same dyno an early non-vvti engine gets around 185rwkw(aftermarket ecu as well) so there's a big difference and the torque is noticeably different to the early engine. Ive even done a few supercharged running the stock ecu for the auto control and aftermarket for the engine.
Motec would be another great option but the most important thing is the tuner is confident in the system that is chosen.
What's modified about the engine? Boost, itb? Or why else do you consider aftermarket ecu?