And the eggs are frequently in places a queen couldn't possibly get (old sewer tunnels), but that could be explained by workers carrying the eggs away to nurture
Yeah, I always thought they worked that way.
Queen lays eggs > lesser Mirelurks fertilize/carry the young away to form a nest > hatchlings pop out, grow up/get stomped out by blue spandex, yadda yadda > repeat. But, since there's a bunch of raiders actually farming Mirelurks, then some of these beasts can probably reproduce even without a Queen. I'll work on a Mirelurk plot as soon as I'm done putting out plots for the vanilla game.
Disasters like increased attacks from a specific animals, like the ones in Wasteland Workshop, are probably possible - I imagine that all someone has to do is use whatever makes the cages tick (and causes the attacks) on the plots.
As for the other ideas: they're cool, but genetics and advanced technology is a little too much. I'd like to keep on a rural/farm theme; advanced technology or Science! may appear every now and then, but it's going to be super-rare.
Don't forget the mirelurk nest quest in Fallout 3 for Moira's Wasteland Survival Guide quest series. Not a queen to be had in the Capital Wasteland, so I imagine them to be some sort of super-lurk, rather than actual mothers like an ant queen.
I second Jose's request for rad-chickens. I'd give the chickens a pretty broad wander range to give them a proper chickeny feel. Just wish their animations weren't so sluggish (cats, too, for that matter).
Yeah! ...but, even if we don't see it, who says there are no Queens in the Capital Wasteland? I mean, Queens are something they came up with for Fallout 4 - but it wouldn't be a stretch to think that the same species you meet in Boston also were in Washington; I'm just thinking that all of this would be so much easier if we had a single Mirelurk species (or if someone in-game explained how they reproduced).
Also, rad-chickens and rad-rabbits are definitively going to be in my Add-On. Probably the first plots I'll do once I decide to switch to Far Harbour. I can't have an Add-On about farms and not add these two animals, afterall!