I think it could be argued that pedals are generally better than build in effects, but it depends on personal taste, too. Another argument for pedals is that many of them have more controls to customize the sound.
As far as batteries, most of my pedals have a battery option, but I never use it, because they run down too quickly. I'd rather not have to worry about it. I'm not sure what you mean about positioning pedals when plugged in, though. If you have more than a few pedals, it's helpful to have a power supply for all, like the 1 Spot. It saves getting a power converter plug for each one.