Strong 2-3 shudders when ICE turns off at stop?

it's trying to find the point for the next start up. could be any part of that system is starting to malfunction.
how many miles on her?

 

Do you get a similar shudder when parked and engine kicks in for battery charging?

 

Perfectly normal... It's the nature of the atkinson engine and Toyota did spend some time modifiying the intake manifold to make this less severe on cold engines in Gen3: Rough engine start | Page 13 | PriusChat

And in that same thread in link above is best explanation of the problem:

"I can duplicate the rough start problem by starting the car when cold, moving it a few feet or just letting the car idle for a few seconds, then shut it down. I thinks what's happening is unburned fuel is left inside the cold cylinders and injectors and it has a hard time clearing it out when you go to start it the next time. I had several other non-hybrid cars that would experience rough starts too because the injectors /cylinders still have cold unburned fuel in them under same circumstances. It only lasts a few seconds and everything if fine afterwards. I'm wondering if the Atkinson cycle of the valves also make it sound worse than it really is?"

Got my Prius with this intermittent problem with 104K miles on it a decade ago and now it's getting close to 280K miles and still no signs of trouble. Suspect previous owner saw this issue as a reason to move on from the car, as it was the only thing wrong with a car that was kept in almost perfect condition in the first 5 years of its life.

 

Would I be right in guessing that it happens after you've been driving for about 5-15 minutes? It sounds like you're in stage 3 of the warm up cycle. There's a point in the Gen 2 warmup cycle where it shuts off in a ragged sort of way and then, once it off and you're waiting at the light, you feel an occasional very gentle little nudge. It was really spooky with my '05 till I found out what it was.