It sounds like you are interested in future capabilities, so I’d say the RPi is going to give you more options in the future. It’s quite a bit cheaper as well ($77 + $35/RPi + SD Card). Of course it’s not quite plug and play, but the preconfigured SD card really makes setup easy. It helps a lot to have some basic linux knowledge (if you have 3 Rpi’s already you’re probably good-to-go). Functionally, they are pretty much the same. With the RPi, you need to access it from another device (computer, phone, tablet) to do anything with it. The ATMega version has a screen and some buttons so many, but not all, of the options can be set from the device itself. It’s kind of nice to be able to see some information without having access it from another device.
If you don’t mind a little extra setup the RPi is what I’d recommend. I did the same thing last year – moved into a new home with an old sprinkler controller and I promptly replaced it with an OpenSprinkler Pi.