I think you're right. Some work has been done on that (but not enough).
For example, my Hybrid Escape has what Ford calls an Atkinson cycle engine. It's not really that at all; what they've done is retard the timing of the intake valve to reduce pumping loss on the compression stroke (some of the mixture flows back into the intake runners).
Also, the throttle is fly-by-wire. You can't do things like rev the engine unnecessarily when the transaxle is in park. You can't power brake either, but then this isn't a performance car either.
Probably the delayed intake closure to which I was referring. It may be that doing that reduces throttle energy waste to the point that there's not much worth harvesting, but otherwise as I said the throttle, if harnessed, would represent better-than-free energy.