Right now, there is more infrastructure around the Arduino than the R-Pi. It may be in 6-9 months time there will be much more support for physical devices on the R-Pi, but right now, I would go the Arduino route. It may be with all of the stuff you have planned, you may eventually outgrow the Mega, and the bigger address space + faster processor on the R-Pi may be needed. Or you create multiple specialized Arduino's that handle specific tasks.
In terms of a universal IR remote, there is this tutorial from Lady Ada (i.e. adafruit): http://www.ladyada.net/learn/sensors/ir.html
Do remember to always have a manual override, in case things go haywire, or your batteries run down.