A Nuclear Breeder/Day Care

[PhantomUnderYourDesk]

Ah, it's nice to see that this issue is serious, and plays around with the player's morals and personal beliefs. ^-^

On the issue of Duplicat, let me make this clear: the user would not get the 6IV Duplicat! It would solely be Nep's, and only used as a substitute parent if two are not used. Furthermore, it could only ever be mentioned that he has it. You wouldn't ever have to see it. 
(...)

I know. Via "spoiling" I meant that I would find it rather unfair that he would own something that the regular player would never have, unless they'd engage in cheating. (Should have made it more clear in the first place, sorry) It would make Nep... even more of a cross-border commuter.

About those unwanted eggs - I guess it depends on one's way to spam for eggs and chainbreed, then. Since I never had any eggs I wouldn't want to hatch, neither in the official games. Or it's just me being finicky... if ever, I'd wondertrade them though, but if you don't enjoy that as you stated, the possibility to give them away to an NPC after obtaining them would be handy.

The collectible aspect - it would indeed be neat to hatch a shiny nuclear-corrupted Pokemon ... but given the boxes filled with non-shinies of the same or even several species, I'm not that sure anymore whether I'd be happy with that thought... Same goes for breeding them in general. Feral or not, they're still instable and corrupted, and should be treated with caution and a sense of responsibility. (At least that's what I think) It's not like I don't own a couple of them by myself, though. However,  it's a on a totally different level whether you own several boxes of the same Pokemon, even if it'd be something morbid like Chainite, or of unstable creatures leaking radiation. (I agree on the point that the stable ones are no harm to the ecosystem.)

Spoiler

(Don't think about PU's endgame too hard - it's a miracle your pokemon aren't mutated or dying as is.)

Well, true story... Pokemon Logic. ._.

That thing about Destiny Knot made useless in that case would definitely make sense. But the nature nevertheless determines quite much whether a particular Pokemon becomes strong or weak. It wouldn't be a suprise if most of the allowed Legendaries found in higher tiers would likely get banned if they'd be breedable.

(...) The main character is hailed by all as the hero who stopped the nuclear disease to spread further, it'd be pretty villainy, or at least, hypocritical of him/her to go breed Nuclear pokemon on purpose

Lolz... they took an example from their mother. CURIE's successor.

(...) but perhaps you could "lawfully" be allowed to breed a limited number of Nuclear Pokemon (say, one or two per species, or maybe 10-15 overall) strictly for "research purposes". (...)

Who would make sure then that that one person stops after that, and doesn't secretly keep on breeding them? In my RP, I solved this issue with a whole research facility where several of those unstable ones are contained in a restricted area, and doing anything with them that's not intended will be punished with harsh disciplinary actions.