The Roku 3 does work with IR remotes. My Harmony remote works fine, though the remote needs a line of sight for it, while the default Roku remote can be used anywhere in my house (or even outside since it is all wi-fi).
Your main limitation for the Roku 3 is no HDMI output on 3 of your TVs.
I have only used the Roku 3 (I have two of them, and they work great), so hopefully someone else can chime in on the Roku 1 and 2.