Oh that? Simple.
1. It's not DLC.
2. They don't get the full pie share as much as say, something like Kingdom Hearts.
3.Nintendo don't have the time and patience to deal with Square's stingyness just to get Geno and Mallow.....for now. (Hopefully that'll change in the future).
4. It's not DLC. I can't stress this enough that Square love having their stuff as DLC in collaborations like these since they get more a lionshare with DLC.
5. They're likely waiting for some sign that it's a guaranteed money maker. Trust me. I know how Square operate with their inane expectations. They'll set up whatever "test" they can when it comes down to stuff.
6. Square are awfully negligible in handling older stuff. See, Brave Fencer Musashi, FFVIII, the works. If it's old and hasn't been continued in some shape or form, they only keep them around on threads of life, some rare exceptions notwithstanding.
7. Square are just unpredictable as fudge with whether they'll do something smart or dumb. Us Square fans thought they finally had their heads onright with the new president after the diablocial reign of the XIII trilogy and for a while they had...until they lost it again recently.
Oh, of course, I only mean DLC and strictly DLC, maybe with a remaster for SMRPG being the most they'd do for non-DLC. Adding Geno and Mallow into anything base game would be very... not like Square. They love their money. That being said, it does make it weirder still how they were able to get those spirits into Ultimate. If Square was as stingy as they were with base game and Cloud, it's a wonder Sakurai managed the miracle of their spirits.
Everything else is a valid point, though. It makes me wonder how well Geno's Mii costume sold for being on a game on a dying system. I fear it might not have been enough for Square to be A-OK with it, which isn't very fair considering the Wii U was failing and Sm4sh didn't sell as much as it could have as a result, but eh. Square ain't known for playing fair.
As for old stuff, man, Square is just odd. The way they shafted FFVIII is definitely among the weirdest things they've done, even though they're revisiting VII, IX, XI, etc. Those getting ports with VIII being skipped is so... so weird.
So weird.
That being said, if I were looking to bring Geno and Mallow back even once to kinda test the waters on their net capital, I'd say that Mario Kart 8 Deluxe DLC would be the best way to do so. Put a nice price point for one or the other or make a combo pack, split the shares with Nintendo, and use that as a test to see just how much money they'd make off of them. MK8D is a highly-sold title, so it'd be dipping into a large pool of possible buyers, casual or not, and they could aggregate numbers accordingly. If it's successful, they can do more with them for other titles as DLC characters, or heck, maybe even see about remastering SMRPG. If not, then at least the fans get one last hurrah before they go into retirement.