The A9 is very much a breakout product - a first-generation action body which, for the first time, demonstrated the viability of mirrorless cameras for shooting fast action, with the ability to keep up with SLRs, but with all the flaws common in early-generation bodies. Updated with the latest firmware, it has the best AF system I've used, but that still doesn't alter its shortcomings in these other areas which affect usability. It is, in effect, a proof-of-concept model - a very high-performing one, for sure, but still a technology demonstrator rather than a fully mature camera. I would expect most, if not all, of these shortcomings to be rectified in a second-generation A9II.
Among these shortcomings:
- Slow second card slot. The system is only as fast as its slowest component, and this is an action camera designed to shoot at 20fps.
- Physically fragile flash mount
- Slow mechanical shutter - only 5fps when not using full electronic shutter, which matters when shooting with flash, since readout is currently much slower than a mechanical second curtain.
- Some readout issues when shooting very fast movement (e.g. explosions or muzzle flash) with electronic shutter. It appears that readout occurs in bands, rather than individual lines, which can cause such fast-moving objects to appear as steplike bands, rather than the smooth rolling shutter effect you get from a mechanical second curtain.
- General firmware issues. I don't mean AF - I mean things like menus, customisation, file handling, etc., all of which impact on general usability. For instance, it would be very nice to have an option for the two SD cards to mirror each other - delete a photo from one and it disappears from both - acting purely as a data redundancy system. Or the option to focus wide open (or at a certain minimum f-stop) and stop down for exposure, allowing for even faster AF, but risking focus shift, just like other cameras. And there are many other, similar improvements which could be made that don't affect technical performance, but greatly affect usability.
None of this stops me using the A9, of course, but it should be seen as what it is - a first-generation mirrorless action camera - rather than as a fully mature system. It is to mirrorless AF what the A7r was to full-frame mirrorless in general, or the 5D2 to digital full-frame - a breakout first-generation product which excels in the area of technology it is designed to showcase, while having other shorcomings which affect its usability in comparison with more mature systems.
I'm very much looking forward to the A9II - I would expect most of these shortcomings to be addressed, while introducing improvements and new technologies making it worth the upgrade. In particular, a resolution increase to 36-42MP (39MP is needed for 8k video when shooting with a 3:2 aspect ratio) would make it a viable replacement for the A7r3 as a do-everything body, while a global shutter would change everything with regards to flash photography.. The first is more likely than the second, but neither can be discounted completely (I think global shutter is more likely to come in the next generation after that, though).