Note: This is probably best for the type of person that only uses their TV for Apple TV (like me) but could work in other situations I'm sure. Also, here's a video if you'd rather watch than read. Apparently The Verge doesn't allow Vimeo embeds.
So I have two remotes: my Apple TV remote, and my enormous Sony remote that came with my TV. The only thing I use the Sony remote for is turning the TV on and off and controlling volume. Three buttons out of too many to even count. Meanwhile, the Apple TV remote has 3 plus a D-pad and I use all of them. It's ridiculous to me to have one huge remote that does so little, and one tiny remote that does the rest. Why can't there be one that does everything?
Upon searching the web for some sort of clever solution, the best thing I found was to use a universal remote. But that involves buying a universal remote and pressing a button to switch between the devices you wish to control. That's stupid.
Now, the Apple TV can use universal remotes by "learning" the remote instead of the more traditional way (as far as I know) which is entering a code that corresponds to your device. Upon seeing this I realized it's really just mapping whatever IR the remote is blasting out to a command. So why can't I map the buttons on my regular TV remote to the Apple TV? Well, you can!
Just navigate your way to Settings>General>Remotes>Learn Remotes and go through the process on your regular TV remote!
From here it's self explanatory. It'll ask you to press up, down, menu, select, etc etc. You pick what you want those buttons to be on your remote. You can even assign playback functions like play, pause, and fast-forward!
Once that's all done you'll be controlling your Apple TV and your TV with just one remote, all without having to tell your remote what device you wish to control. It really has transformed the experience for me.
I'm uploading a little video walkthrough and will add it to the post when it's done processing.
Hope this helps you guys out!