I prefer Wi-Fi. It's a roots thing. I prefer actually raising my Pokemon, dealing with their imperfections and putting them up against other teams. It's also much harder for non-RNGers to do certain things like Shiny-fy Pokemon, or get the right Hidden Power type. It feels more natural.
I do use Pokemon Online, although mostly as a tester before I go for the real thing. Breeding for Wi-Fi
is time consuming, so it does save testing/learning time to use Pokemon Online, if only to see what tweaks need to/can be made beforehand. For example, I could run a Dragon Dance Scrafty, and realize I only need Bulk Up, but I also need Ice Punch, where the Dragon Dance Scrafty didn't have Ice Punch. Pokemon Online lets me buffer things down to as close to perfect as I can get them, and then I breed them.
Like Blue Harvest said, PO is the Hyperbolic Time Chamber (DBZ Reference FTW! XD). You go in, train, speed things up to see how things go. Then you take what you learned, what you gained, from it to the outside, real world (Wi-Fi Battling).
But that's just me I guess.