I'm in Georgia and we also have terrible thunderstorms, and I've had a couple of EZFlora failures. During the winter months I unplug the connectors from EZFloras, and unplug the units as well, as the grass doesn't seem to need watering much then anyway. That's the only solution I can think of. Fortunately SmartenIt has (or has had, at any rate) a $40 refurb fix/swap fee, so it's not terrible to get them replaced.
I have looked at the insides of my replaced RainBird Irrigation Controller, and they have what appears to be surge protection built in on each line. It's too bad SmartenIt can't build a similar box with built in surge protection.
All this said, setting up an Arduino sounds like an excellent idea. The whole thing is so simple... just a few relays. I currently use Berkinet's excellent Phidgets plugin and several Phidgets devices to control my water on/off valves and to read a couple of water meters. It would be great if a motivated soul could write an Arduino plugin that would accommodate different devices, as the Arduino devices are much much less expensive than Phidgets. hint hint...
