I'm right in the middle of installing a 3.6L in my 914 as we type. As others have mentioned, it's only becomes troublesome if you are trying to use the original ECU. Since the all of the suby cars equipped with said motor are running CAN Bus communications, one must bring in ALL of the different modules to trick the system into thinking it's still in a Subaru. There are several different stand-alone ECU's out now that will work with the variable valve timing on the 3.6L, and while a little $$$ I'm not sure they would cost a heck-of-a-lot more than the complete wiring harness+computer modules from the original car.
If you talk with the guys down at Outfront they'll probably steer you towards an AEM Infinity system. Their new unit is priced in the $1,500 -$2,000 mark depending on what wire harness options you go for. All-in-all I'm pretty impressed with the AEM ECU and will be going that direction myself as soon as the funds materialize. After that, everything is pretty much identical to the EZ30D motors...except you'll have more horsepower/torque
Also, something to consider regarding the 3.6L. It's really not a good platform for forced induction. In order to get the additional displacement, and keep the same footprint something had to give, and the crankshaft isn't quite as beefy as it is in the EZ3.0L variants. As such, the crank shaft is actually the weakest link (not the asymmetrical connecting rods) and will likely be the first thing to go with forced induction. This info comes from the guys at Outfront, not my own experience. Anyways, if you are seriously interested in forced induction now (or in the future) you might want to consider the EZ3.0R.
Let us know what you decide!