I've switched between a variety of thermostats in my home automation experience: Insteon, 3M WiFi (junk), Honeywell WiFi (unreliable due to poor network implementation), Trane Z-Wave (never had an issue).
In my new home, I'm using the newest Ecobee with remote sensors in other rooms. As noted by Joe (developer of the Ecobee 2 plugin), as a general rule you won't use Indigo to directly control the thermostat. Ecobee has done some pretty amazing work with making their thermostat intelligent - working with remote sensors to determine other room temps and occupancy. Pair that with "Comfort Settings", which I guess are much smarter version of the old "programs" in other thermostats, the Ecobee this far seems to do a really good job of keeping the rooms in our 2 story condo at the temps we want based on scheduled changes between comfort changes. I have one override Comfort Setting ("Extra Cool") that I can easily toggle from Indigo when the upstairs gets a bit too warm (it's somewhat ironic that it's easier to do on-the-fly toggling of comfort settings through Indigo and the plugin that it is through their app or at the thermostat itself). I also get a rebate from Austin Energy for using a thermostat that they can commandeer during high energy use periods.
I'm waiting to pass final judgement until August & September when the temps here hit 100°F - we'll see if the Ecobee can do the necessary adjustments to keep the condo rooms comfortable using it's logic.