While who knows if Marvel would ever consider collecting this stuff in omnis, you really should email this to Jeph and Cory in the collections department or make sure they see it on the masterworks forum. Just tell them to file it under "helpful possible future omnibus mapping strategies."I agree, this material is amongst my most-wanted omnibus books!
I'm not sure I'd go with the all-in method like you have here. Some of the books get pretty disparate at points and don't especially make a good read ganged together (Astonishing, New Mutants, Young X-Men) while others would sell better all as one run (Carey Legacy), and some stuff just doesn't need this treatment (Prelude to Schism, bleh). Oh, plus - since Necrosha wasn't a direct crossover, its issues can easily be dispersed to their respective books.
I could see it going something like this, which tends to group like-with-like a bit more. I think I've left out a few little mini-things and one-shots (Serve and Protect, for sure), but otherwise this would be a mega-solid collection of the core threads of the period.
New Mutants: Regenesis
(-nfernus #1-4, New Mutants #1-11, 15-21, 25-50, Exiled #1, JITM #637-638. Age of X doesn't really have too much impact on this title compared to Legacy and Carey wrote all of the crossover issues, so it's better there. Plus, X-Infernus is a good prologue and explains why Magik is there)
Uncanny X-Men: Endangered Species (I could also see the argument for splitting this into "Manifest Destiny" vs. "by Matt Fraction")
(UXM #487-491 & 495-512 + Annual 2 + All of Endangered Species (about 6 effective issues) and Messiah Complex (13 issues), plus material from Divided We Stand (2008) #1-2, X-Men: Manifest Destiny (2008) #1-5, FCBD, Nightcrawler #1, Eternals #7-9, Runaways #10)
Uncanny X-Men: Second Coming
(Basically, Utopia (364 pages) + Nation X (360 pages) + Second Coming (392 pages) + Second Coming: Revelations (208 pages) = 1324 pages, which is still a hair under Marvel's biggest omni, and would be a massively satisfying read.)
Uncanny X-Men by Kieron Gillen (let's lean into his hotness with fans at the moment, eh?)
(UXM #526-544, 534.1 & Ann3, UXM #1-20, Heroic Age: X-Men, X-Men: Regenesis, Generation Hope #1-12, Steve Rogers: Super Soldier Annual 1, Namor Annual 1. I'm not sure you could squeeze in AvX: Consequences. You don't actually need Schism to understand what's happening here, especially with the GenHope Schism issues.)
Wolverine by Jason Aaron Vol. 2
(Wolverine (2010) #1-20, 5.1, & 300-304, plus Astonishing Spider-Man & Wolverine #1-6, X-Men: Schism #1-5 (bonus that's not in the complete collections!), and material from Wolverine: Road to Hell)
X-Force by Kyle & Yost
(Just the pair of X-Force OHCs + X-Force Necrosha material; easy)
X-Men by Mike Carey, Vol. 1
(X-Men #188-204 & Annual 1, Secret Invasion: X-Men #1-4, X-Men Legacy #208-225, Wolverine: Origins #28-30, X-Men Original Sin, and maybe material from X-Men: Pixies and Demons - Director's Cut (2008), X-Men: Divided We Stand (2008) #1-2, and X-Men: Manifest Destiny (2008) #1-5. Most X-books break best around Second Coming, but this book has a better break with Rogue gaining control of her powers.)
X-Men by Mike Carey, Vol. 2
(#226-234, 238-260, Giant-Size X-Men Legacy, Age of X: Alpha, New Mutants #22-24, and Age of X: Universe #1-2 - yes, I'd include the pair of Utopia issues and the Necrosha issues, they work fine on their own. We could also pad this with X-Men Origins: Beast (2008), X-Men Origins: Gambit (2009), Wolverine: Firebreak (2008), and X-Men: No More Humans OHC)
X-Men: Regenesis OHC
(X-Club #1-4, Magneto: Not a Hero #1-4, Wolverine and the X-Men: Alpha & Omega #1-5, Generation X #13-17 - you could even include the garbage dump of Prelude to Schism #1-4, if you're feeling malicious, and also Pixie Strikes Back #1-4, Psylocke #1-4, and any other Heroic>AvX era minis or one-shots I'm forgetting just for solid coverage of the period.)
PS: I'll be back with a more refined look at this plus A LOT MORE X-Men omni suggestions later this week, so no need to hurry up and vote