I have both; the HHKB Pro 2 for several months, and the Kinesis for a couple of weeks. I don't have RSI or any other medical conditions which might influence my decision.
Unfortunately, I like both. I thought for sure that I would end up liking one keyboard over the other, but so far this has not been the case. The key switches on the HHKB are amazing. The switches on the Kinesis are different, but also feel great.
I only feature that could make me favor one keyboard over the other is ease of use of the cursor keys. But the cursor keys are equally frustrating to use on both keyboards.
Just my 2c.