I would only consider flat pedals (probably mixed flat on one side and clipless on the other) if you're mostly planning to use the bike with "normal" clothes and shoes. In which case, a road bike isn't the best tool for the job IMHO.
I'd just buy Shimano M520, as they are really cheap and durable. Probably not ideal if you're weight-obssesed or want to use SPD-SL though (I like being able to walk, so SL's are a no no).