I know you were talking about why they don't have MEs for ALL Pokemon, but you took the fact that we don't have 3D models for all trainers as the hint (the 'why') that Game Freak must be limited to a maximum of 28 Megas this gen. I don't even consider having trainer 3D models as a pre-requisite for adding Megas. It's like how Game Freak could probably finish adding evolutions for every single stage non-legendary but they never had the intention to, and instead constantly add more single stages for every new generation to leave things open. Likewise for Megas, even if Game Freak accelerates the process a little such that we can eventually have Megas for every Pokemon over the next few generations, they won't do it. Whether we get 3D NPC trainers is a mutually exclusive issue altogether.
As for how Megas would exclude the addition of Cross-Gen Pokes later down the line, that's anyone's guess. Megas aren't permanent upgrades, and there's always a small chance that cross-gens can still be added as a branch from Mega. If not, I guess some unfortunate critters with unimpressive megas probably have their fates sealed.