I'd say from a reliability standpoint it's a toss up. Stock HEI or Pertronics are both completely dependable.
About 20 years ago I built my 350 with a Mallory Unilite which was horribly unreliable. That convinced me I didn't want anything fancy, just something that worked - so I switched to a stock GM HEI and have never had a bit of trouble. And parts are available everywhere which is a plus.
On my 68 Ford 360 a Pertronics kit was the cheapest option, so I put one in and it has performed flawlessly for about 5 years now. If I were to do a V8 now, I'd probably lean toward the Pertronics, since it will fit in a small cap distributor, look more vintage, and provide better clearance than a large cap HEI. With an inline six, I'd go with whichever is less expensive since they both perform equally well.
