If you're talking about Otocinclus rather than the neons here then the 'gene pool' (I assume you're referring to inbreeding depression?) shouldn't be an issue as they are, as far as I am aware, all wild caught. Therefore if they have survived to reach adulthood in the wild they should certainly be genetically fit.I suspect it might be gene pool or treatment (antibiotics etc.) when juvenile determining how long they can make it?
I think that as they are starved before shipping some simply don't start feeding again and waste away unless they are immediately put in an algae filled tank, with algae they will eat. I've found mine are really only keen on diatoms and green algae - they won't touch my BBA or BGA when I had an outbreak.
Of my last batch of 6, one died after about 5 weeks while the others are still going strong months later.