The Elk or HAI systems definitely have the ability to be your complete home automation system. HAI has their own offerings to make up a complete system, and also interfaces with the common systems out there. Elk doesn't really have their own thermostats or lighting controllers, so they just build in the ability to connect to 3rd party systems. From what I've seen, there's little advantage to one over the other unless you want a complete HAI system out of the box with their screens, controllers, etc - since they do pretty much cover every base. That said, I use an Elk because they've always supported DIY, where HAI only recently started to.
As said above, the M1 uses a Serial Port adapter to connect to most automation devices (thermostats, lighting controllers, etc) - to help, here's
a link to the manual that might give you a better idea. Elk also now has a native UPB controller you can buy that connects directly to the databus vs. using an interface module with a serial adapter. I don't think there's any difference in functionality.
For thermostats, Elk can do Z-Wave (I'm not sure which models or if there are limitations) and it can do HAI, AprilAire and RCS's serial thermostats; so you have plenty of options, especially in new construction.
For me, the Elk is 90% of my automation with Elve software adding in additional rules and better touchscreens. It lets you start small and build up. Also, as said above, it's pretty sweet to be able to have your security system respond to lighting events, or lights turn on as doors open, or porch lights turn on if someone rings the doorbell after they've turned off or if someone leaves the house late at night; etc.