I've got both. Here is my take on it.
If you strictly want 2M and 70cM or D-STAR, then the IC-9700 cannot be beat. If you want something that can do bands other than 2M and 70cM then the FT-991A is your rig. Note that the FT-991A, while it can do more, it does not do more best.
Here are the biggest disappointments to me about each transceiver. Keep in mind that both of these are awesome radios, but here are things I have discovered about them that I do not like.
FT-991A:
1. Cannot scan memories across 10M or 6M bands without a VERY audible relay clicking continuously. You can scan 2M and 70cM together fine, but going into or out of the 10M and 6M bands will drive you nuts with the clicking. So, if you want to scan 10M FM, 6M FM, 2M FM, and 70cM FM, you will be disappointed.
2. 2M and 70cM bands use the same Mitsubishi MOSFET PA that the FTM-100DR and FTM-400XDR uses. I have personally killed at least one of these MOSFETS in each of the three mentioned radios before. Yaesu SUCK at heat management and the FT-991A is NO EXCEPTION.
3. The cooling fan is too loud. Granted that this is a nitpick gripe, but when my computers are quieter than my radio that is sitting idle, I have a problem with that. Note that the 991A is not loud the instant you power it on, but if you leave it on all the time you will notice it. I dare not attempt to replace the fan with a quieter model, as I don't want to worsen the cooling that it does provide.
IC-9700:
You cannot use more than one band in the top or the bottom display. You cannot mix bands in a memory lineup. You cannot scan more than a single band in a scan list. This radio separates the three bands completely. You can select any two and assign one to top and the other to the bottom and that is it. I wanted to park the bottom on 2M SSB and then scan 2M and 70cM on the top side of the radio. Nope! You cannot mix bands. Now, I can monitor 2M SSB on the bottom and scan 70cM FM on the top, that works fine. But in order to scan two bands you must use both the top and the bottom of the radio.