Has she tried an EOS-M with the 90EX onboard? It's still small, but has a much more reasonable flash. The flash output on the M3 is a joke honestly, all pop up flashes are really not worth having, but that's just my opinion I suppose (and fully aware that the 90EX's output is about the same as a standard popup on larger bodies).
I still use and keep an EOS-M (first gen) with a 22 F2. The EOS-M can focus quickly, but the 22 F2 cannot. That's the issue. The moment you put a faster focusing lens on there, it's pretty fast. I tried it with my 35 F2 IS and 85 F1.8 and it was very fast, did a fine job. Just was "big" of course.
Unfortunately if your wife wants compact and wide aperture, there's not a lot of options without getting a bridge basically, or looking into M43's cameras. Trying to get those features on an APS-C sized sensor is going to require big glass, due to sensor size. So you will always hit the wall with this one. You may get a small body and the right features (wifi, flash, etc), but then end up having to have a big bulky lens to get F2.8 (this would be how Sony ends up). But again, if you're trying to get fast aperture on a larger sensor, it will be a larger piece of glass. So you either need to get a smaller sensor, or slower glass.
I just tested the EOS-M (1) with the EF-M -> EF adapter and a cheap EF-S 18-55 STM, and it focuses fast, much faster than the 22 F2. But, it's hardly compact, since the lens has size, the adapter adds to it, but you keep a small body, if that matters. I'm not sure which STM motor version is in the EF-M 18-55, but the EF-S 18-55 STM focuses quite fast, and dead silent, it's nice actually. So if the EF-M 18-55 has that same motor and is also fast and silent, it would be a fine option, just not F2.8.
I think the M series would be fast enough for general stuff, if they would release the 22 F2 STM with a faster focusing version motor. Right now, the 22 F2 STM is slow to focus, just like the 40 F2.8 STM and 50 F1.8 STM. All three of those are kind of slow, you can totally hear them, etc. But, when you listen to the 18-55 STM, 55-250 STM, etc, they are very fast to focus and completely silent. Definitely some differences in the STM motors in various lenses.
But it is clear to me that the slow down point of the M series with the 22 F2 is the 22 F2 itself. The M focuses plenty fast. The limitation is more the lens you're using.
So, next step, if the above doesn't have anything in it that rings as an option, either go with Fuji, or look at a M43 camera body and lenses. The GH4 for example and a fast zoom. Small, fast, and even weather sealed. GH4 with a 12-35 F2.8 would be great, it's costly, but great. And again, here we are hitting that wall with F2.8 requiring big glass. But the 12-35 F2.8 is the equivalent of a 24-70 F2.8 on full frame. So it's a compact version (if that can be said) of that, all weather sealed, fast, 4K capable, flash, etc. It's about the size of the SL1. So it's still small.