What sort of HVAC problems in the Flex? The blend door motors that control airflow fail quite often in these. Not an expensive part, but often a lot of labor.
Many people with your list of criteria have been buying the Subaru Outback, which is really a lifted wagon. Plenty of legroom, but still possibly smaller than you're looking for. Owners have reported oil consumption issues with the 2013, but not for more recent model years.
Either Jeep Cherokee or Grand Cherokee is likely smooth and quiet enough, and both are designed for off-roading. My concern with either is long-term reliability. For both the new / updated 2014 model often required repairs, but the 2015 and up have been good so far.
If long-term reliability were your top concern, I'd suggest the Toyota Highlander. It's not designed as much for off-road use as the others, though. For that Toyota offers the 4Runner, but the 4Runner has the sort of ride you're seeking to avoid.
Lastly, GMC has an all-new, midsize Acadia for 2017. But an all-new GM vehicle in its first year is risky.