We've been trying to make a similar choice. I love the look and feel of Nest, but it's so locked down to Google it's hard to justify over a Honeywell or similar system that will work with our HomeKit house.
We've got Ikea lighting and outlets, some general HomeKit bits and quite a bit of Elgato Eve stuff that all connects to HomeKit; meaning Apple's Home App (or Siri) on our phones is the main controller for anything smart related, and it's all in one place.
Ironically the only smart stuff we have that doesn't fit that ecosystem is our Nest Protects (fire alarms) which are excellent pieces of kit, but just don't fit into the 'smarthome' that we've built up. I'm not sure I want to add to that split with the Nest Thermostat when it's something that we'll likely be controlling quite often as the house is old and does heat up a bit funny (in a terraced street so often our heating pattern is highly dependant on how much the neighbours are heating their houses too).
The ability to control it through a central hub on our devices (rather than the physical thermostat hardware) is probably more of a pull than a nice looking 'stat and probably (for us) more important than Nest's 'learning' features. But I totally agree that almost all the the other smart systems have ugly-as-sin thermostats.
Elgato and others do smart TRVs that work independent of your thermostat which we're looking into now as an option (HomeKit compatible). Works out a lot more expensive, but would give us individual room smart control. I'm not sure if they'd mess with Nest's 'learning' features if you had them together though?