The only easy choices are Cyclops and Storm, for the O5 and ANAD teams, respectively.
Cyclops and Storm are forever X-Men IMO. I can see Kurt and Logan doing other things that better suit them, but Cyclops and Storm will die X-Men and I feel like those are good candidates to lead a team of generational representatives.
Rogue has an eye for redemption and I think her work with the Avengers will make her the most connected to the non-mutant heroes and perhaps rub even her longtime friends the wrong way. Still a mutant hero through and through, she'll have a perspective that challenges her teammates.
Rahne, who is like my 6th or 7th favorite New Mutant (s/o to Rictor, Dani, Berto, Doug, Illyana, and Tabitha lmao) was my choice for her generation. For one, I wanted someone with a physical mutation. I wanted someone that not only showed the turmoil of mutant life but also be a source of hope and mercy.
My 90's recruit choice was just as difficult as my NM spot, but I went with Bishop. I just liked the idea of him working with pretty much every member of the cast and bringing out different facets of his personality. He is a doomed future living in a better one and I think that his personality could have a lot more texture working with Scott, Rahne, and...
Monet/Penance, my Gen X choice. She's my fave so duh, but the perfect mutant whose arrogance is cursed with an untouchable exterior spices up most group dynamics. I think she'd be the most eager and capable to prove she is just as strong as her superiors, but of course has a lot of issues to work out before leading
anybody.
My Academy X person is Prodigy. He's increasingly iconic and his quest for data has shown to lead him dark and disturbing paths (corpse garden, anyone?).
Potential Swaps: Rahne and Bishop for Rictor and Marrow.