ischmitz, you've summed it up nicely. I would stick with late 964 if I were going to further hotrod the engine, or a 993 version if no further engine work was envisioned.
The 993 hydraulic lifters are a huge plus for a street driven engine. I also think that the internally balanced crank and lighter rotating components are an asset. Another plus is the MAF setup on the 993. On the other hand the heat and electrical hookups are somewhat more difficult. The euro non obdII version of the 993 sounds very intrigueing!
Here are 2 relatively recent threads;
3.6 swap1
Best 3.6 to transplant