Logitech Harmony Remote Clone

I'm not sure I've come across anyone making a remote control with Espruino (a few have used it as a remote control for phones/tablets/etc though).

For IR, there's a bunch of info already:

• I used one to control IR light bulbs: http://www.espruino.com/Puck.js+Infrared
  
• There's a Pronto Hex decoder: http://www.espruino.com/pronto
  
• And info on decoding received IR signals: http://www.espruino.com/Infrared+Remote+Control
  
  

Transmitting via Bluetooth shouldn't be a big issue though.

I guess a good start might be http://www.espruino.com/Pixl.js - while it's not ePaper it's an LCD with a backlight and a good battery life (should last around a year on 2 AAs). It has Bluetooth LE as well and should be pretty easy to attach a keypad to.

remove the Pi altogether

It should be fine to do that as well. Either you could add an IR transmitter to the Pixl, or could just add a Puck.js in your TV cabinet (as that has an IR transmitter) http://www.espruino.com/Puck.js

If you're adding a Puck.js then http://www.espruino.com/Puck.js+Infrared has some info on making a Web Bluetooth page to send out IR signals, so you could then just use your phone as the remote :)