That's not much of a downside; that's barely an inconvenience. Chuck them into an accessory box like most of the accessories that also can't be stored in/on the figure these days. Still rather have them than not have them.
Alternate heads have been one of my most requested things for some time. In theory they're easily implementable, as long as the neck joint is simple for popping on and off (a standard ball joint should be fine). And let's not have any of that "it's actually an alternate mask, the base of the head stays on the neck" nonsense from the troop builder pack.
Problem is, what I'd prefer are entirely different heads (perhaps even the ones intended for pretools) as opposed to the same head with a different facial expression or detail color or degree of battle damage. Like, Bumblebee having an alternate Bumper head or an Earth mode Prowl with an Autotrooper head. So that's probably something they're even less likely to do. But it'd be nice to at least get, say, the same Ratchet head in cartoon and comic colors. Options are still good.