Sigh...well...
STOCK FOR STOCK (ECU AND INTERNALS) AND N/A (With some turbo/sc notes) Drop in and go...
5vz vs 3vz
ECU -
The 5vz is limited to 5500rpm even though it is capable of higher. The 3vz-fe ecu is less picky when it comes to CEL's and crap, also easier to throw a auto ecu into the car without as many problems. VERDICT: 3vz-fe
Intake Manifold -
The 5vz has a great intake manifold but only great for lower rpm towing torque! For the mr2 this would lead to a very crappy power band. HOWEVER when boosted the intake manifold works just fine providing airflow throughout the rpm range as seen in supercharged 5vz's which see no drop in hp even at its 5500rpm redline (nobody has gone higher). The 3vz-fe intake manifold is of a better design when its put into a car application it has the variable length runners which help give air down low and into the mid-upper rpm range while providing a perfect spot for a turbo intall as it faces the tranny vs the 5vz's faces the trunk 
BUT ide like to add there are some failry easy things you can do with the 5vz to match/beat the 3vz-fes intake manifold...but that is for later VERDICT: 3vz-fe
Head -
Once again due to the original design of the engine (to be put into a truck) the 5vz's cam profile is designed for the low/mid range power band as well as the head intake and exhaust ports made to provide great low/mid range torque. With that in mind though there is much you can do to turn this around as this designs makes a great base to build your own setup with.
The 3vz-fe has a higher flowing head and a bit better cam profile which in the end helps this engine rev up to its 6800ish redline...while it pretty much dies after 5500rpm....but still beats the 5vzs dead hp after 4000rpm...: VERDICT: 3vz-fe
Block -
Well here the change occurs...while BOTH the 5vz-fe and the 3vz-fe have great internals and an AMAZING 1.8:1 Rod to Stroke ratio (and i mean amazing) the only major thing that sets the 2 engines apart is size....the 5vz takes the win with .4L more displacement and that as we all know makes a big difference! Other then that the 2 are pretty damn the same thing 
Verdict: 5vz-fe
Ignition -
Here you got the wasted spark DIS system from the 5vz and the 3vzs disti single coil setup. I cant say anything really negative about either setup other then the 5vz dis looks much cleaner....i cant say that the 5vz is BETTER because people can argue anything, BUT since this is stock for stock comparison and not modified i would still give the 5vz the win for the fact its less maintenance then the disti type, less moving parts and cleaner combustion (wasted spark). Although in a boosted/high rpm app IF the ignition system needed to be stronger the 3vz-fe would be easier to upgrade for most people (larger coil :P) Verdict: 5vz-fe
Fuel System -
Both are seq injection, both allow for a bit more upside (injector wise) as for flow both are pretty much the same. Verdict: TIE
Exhaust -
The log type exhaust manifold of the 5vz-fe makes it pretty easy to build a Y pipe setup to the stock muffler or build a turbo manifold. Pretty simple stuff. The 3vz-fe one is a bit worse of a design, right from the bat but aint to hard to adapt from what i have read and seen here. Verdict: 5vz-fe (just easier)
So overall...stock vs stock N/A...the 3vz-fe will win when you just want to drop in and go.
Time and time again I will say that when you compare these engines with after market parts they will all handle the same boost and they will all flow withing a few % of each other...but in the end the 5vz will come out on top just because of that extra displacement...ALL these engines were built on a similar design even the mz's...to compare it all with forged everything is pretty pointless as all the engines have seen high HP with no problems.
In the very near future i will be showing off what things you can do with the 5vz to make it kick all 3 motors asses
With just a couple changes to make them = to the other car based v6's