Many systems I've worked on can be written as embarrassingly parallel with synchronized checkpoints for a relatively small cost if they're not serial, but yeah, the middle ground is hard. That's the nature of the beast though. Imagine trying to rearrange the instructions in your program the same way. You're going to get all sorts of wacky behavior unless you invest an enormous amount of effort into avoiding problems the way superscalar CPUs do.

Relatively few programs truly need to operate that way though and they're usually written by people who know the cost of their choices.