2013 Prius 3, ~ 60k miles, flat spot on acceleration, comes and goes.

I've never thought of that, but yeah, maybe it is? How many miles on it? Assuming average miles on a 2013, it's probably time to remove the intake manifold, clean everything out. That process hopefully should dispel any minor intake vacuum leaks. For sure clean the EGR passageways too. Further on the EGR:

Turn your attention to the EGR (Exhaust Gas Recirculation) Pipe/Valve/Cooler. The pipe (stainless steel tube between intake manifold and EGR valve, on driver's side of engine) is by far the easiest to access, and once you look at the inside of that you'll have some idea what the rest will be like. Carbon build-up is the issue.

And then, Oil Catch Can?

Watch @NutzAboutBolts videos, pinned in 3rd gen Maintenance Sub-Forum.

Good thread:

EGR & Intake Manifold Clean Results | PriusChat

Another:

Oil Catch Can, Eliminate that knock! | PriusChat

 

at any typical speed?

 

I have watched some YouTube videos on showing live diagnostics to trace a hard to repeat problem, maybe you can try it out to trace it

 

I've heard spray WD40 around suspected vacuum leak areas, listen for engine stumble. Basically if air is sucking in somewhere, it draws the WD40 in, causes a stumble. Sounds messy though. Maybe you could use something cleaner, some spray with non-combustible gas, that doesn't make a mess but alters the idle??

 

Chuckiechan, I would suggest that it is most likely an issue with EGR passages based on your description. It is also possible it could be a spark related issue due to low coil output for a single cylinder or a spark plug that is carbon tracking, but at 60K miles that is a little early for a spark plug. Since the stumble doesn't last very long at this point the misfire detection logic probably can't see it yet, but if it gets worse you should get a check engine light with a misfire code.
I would suggest that the individual EGR passages in the intake manifold may be starting to plug. When this happens the passages that are restricted the most receive the least amount of recirculated exhaust gas, and typically the one least restricted gets more exhaust gas than it needs or wants.
The EGR system was designed to reduce combustion temperatures by introducing "dead air" that slows the combustion flame front. The recirculated exhaust gas dilutes the fuel air mixture in the cylinder and makes the flame search around the cylinder to find the fuel to burn. If you introduce too much EGR gases into the cylinder then the flame has a hard time finding the fuel and the engine misfires.
If it was me I would start by removing the intake manifold and cleaning all the passages. Even if this doesn't fix the issue, your not wasting your time as this is something that should be done at this point. Take note of how each passage looks. The one least plugged is getting more EGR than it should and should be the cylinder that is misfiring.
If this cleaning doesn't fix the issue you have a choice to wait and see if the problem gets worse and helps you out by flagging a code, or start looking at the ignition system.
In my opinion a vacuum leak can't cause the symptom you are describing. Vacuum leaks that are large enough to cause a misfire or stumble will be loud enough to hear and typically cause a high idle. If you really think it could be a vacuum leak then search the web for "Vacuum leak propane enrichment". This is how we safely looked for vacuum leaks when I was a tech.

 

Maybe step one: check the condition of the EGR pipe. Because, it's so easy to get to. 60K miles is not a lot though. See @NutzAboutBolts video #16, linked here:

Nutz About Bolts Prius Maintenance Videos | PriusChat

 

I had/have the same problem. I call it a delay in acceleration. Do you notice that the hybrid system is not functioning normally when your experience this vacuum, like the car does not go into electric mode when it should or that engine holds higher RPMs than it should when your foot is off the accelerator? I've taken it to the dealership several times, they don't believe me or care. it's funny to see all the suggestions from people on here when the dealership had no thoughts at all.

 

“It” being the original flat-spot-on-acceleration issue?

Doubt it. 3 to 6 months, from what I’ve read. Ethanol spiked gas (virtually all) is more prone.