Two arguments against epoxy for repairs that hold up are 1) price and 2) polyester doesn't stick well to epoxy. So, if you think you might want to use polyester in the future then avoid epoxy.
Yes, but there's also arguments that are more to do with what's practical.
If epoxy is chosen as the preferred resin, then one is comitted to adopt an epoxy based system thereafter due to the polyester -> epoxy adhesion issues.
For example, one would be precluded from using the commonly available chopped strand mats.
One would also need to use an epoxy based filler to replace the typical polyester based 'Bondo' or the like.
And as mentioned previously, future repairs would likely be problematic.
Unless you know all the epoxy repaired areas going in, it's a crap shoot. You can't visually determine which areas are epoxy and which aren't.
IMHO, it's not so much the narrow question of which resin is "better", but more the wider perspective of what's most suited.
There's a plethora of chopped strand mats, fillers, fine skim fillers and spray polyester fillers all aimed at a polyester based repair for the automotive industry. It's all a well trodden path, and compared to epoxy based systems, far cheaper.
I'd have to see something very compelling to ditch that well worn path, I reckon.