That has been a topic of much debate recently. It used to be that the hot issue with strokers and their corresponding rod length used to cause a rod pin intersection with the piston ring groove. This in turn, was known to cause an oil consumption problem. Most manufacterers have worked around the intersection problem and have come up with various ways to cure that problem either by offsetting the wrist pins or using rings that are able to seal well regardless of the intersection. The only real advantage to going with a smaller stroke thiese days seems to be the reduction in rod angle. A less steep angle means less linear side stress on the portion of the piston facing away from the crank journal. The reverse side of that is the number of strokers out there that run reliably for many many miles regardless of the rod angle. Like anything else, reliability has allot to do with the quality of the build. For me... I tend to lean more towards slightly 'less steep' rod angle and give up a few lbs of torque for a better chance at increased reliability. My primary concern is use on the street with as much durability built in as possible for the addition of forced induction (namely my Kenne Bell). If I were building a track only car, I'd go with the largest stroker I could get my hands on and stack forced induction ontop of it to boot. So it comes down to what you intend to do with the motor. I saw someone else on this forum post something that in most cases makes a lot of sense. It was something like:
Cheap / Fast / Reliable.... pick two and build along those lines because it's nearly impossible to get all three. I'd like to give credit to whomever posted that but don't remember who it was.
Hope this helps.