I'm now using a 90D (APS-C) and an EOS-R (full frame). I changed primarily to have a
fully electronic shutter in both full frame and APS-C. For continuous light this is fantastic and I would not want to go back to any type of mechanical shutter.
But... the reason I asked about flash is that Olympus is the only one that has cameras (not all) that offer a flash sync signal with a
fully electronic shutter (as far as I know). It is severely limited in that the sync speed is (was?) only 1/20 second, but there are still ways it can be very useful. Some folks say that low power flash has extremely short duration so vibration is not really an issue with flash. Maybe as far as "sharpness" is concerned, but something that really bothers me is the vibration between shots when shooting a stack. If you are working with a delicate subject (especially in a water mount) the shutter induced vibration between shots is often enough to slightly jiggle and move the subject in the water. Not good for stacks! Or you might be patiently waiting for a live subject to pause so you can rip off a few shots to do a short stack, but the shutter commotion will cause it to move. Obviously your subject matter will determine how big an issue this is. Other cameras will differ on how the mechanical shutter is implemented for flash. On the EOS-R the flash is fired using a (non-mechanical) EFSC, but the exposure is terminated with a mechanical shutter closing and opening. It's pretty smooth actually. On the 90D (and I think many other cameras) the shutter closes, reopens, flash fires, shutter closes to end exposure, and then re-opens for live-view. I'm not crazy about that. But it does have a built-in flash that can be set to a very low manual power setting which I do use to trigger my main flash via an optical slave. Fortunately my working room is quite stable, and I prefer continuous light unless I have an active critter. I'm finding that with the fully electronic shutters I end up using flash less often.
A big caveat recommending cameras is that due to a considerable investment in Canon EF glass I am most interested and familiar with Canon offerings. There are some great cameras out there now but I am not familiar with the intricacies of their operation. Hopefully others can provide useful info on other manufacturers offerings.
So. For APS-C you might want to consider the 90D or the EOS M6 II. Both have a 32.5Mp sensor. The 90D, while a DSLR, becomes essentially a mirrorless camera when used in live view. The specs and features are nearly the same between these two when the 90D is in live-view. I actually sort of like the 90D "hybrid" design because when I am outdoors I really don't (yet) want to give up an optical viewfinder. (The M6 II can use a removable EVF... don't know what it costs). Both can be fully tethered with the Canon Utility software. For non-microscope shots (both scenic and closeup) they both can do "focus-bracketing" and I find that to be a fantastic feature for acquiring an image stack. (Other manufacturers have this as well. I've used it on Olympus Pen F MFT and it is great there too). At 32.5Mp you'll see more noise than your 15Mp 50D, but more resolution (if the optics are up to it!). If you do direct projection with something like a good 5/0.15 or a 10/0.30 this pixel density is not overkill! (But with higher magnifications it definitely is
)
The EOS-R makes a nice full frame on a microscope. The dials and buttons drove me nuts for awhile, a real departure from typical Canon controls. But they are highly customizable, and I have made peace with them, and have things set up as I like. Since I need to use a 2.5X NFK photo-eyepiece with the BHS microscope where I use it, 30Mp is plenty for anything I'll throw at it.