Full disclosure: I'm a big Pocket fan, and a big Instapaper anti-fan.
I like how Pocket is a first-class citizen on all of the platforms I use, not just iOS. I know Instapaper has an Android app, but it sucks.
I prefer the design of Pocket over Instapaper. I'm not a designer, so I can't comment on which is actually "better", only which I prefer.
I do prefer Instapaper's business model. I would like a chance to pay for Pocket.
Finally, I am not a huge fan of Marco Arment, and would rather support Pocket than him.
I've never tried instapaper. At some point I got lazy and stopped marking stories as read on Pocket/RIL and now I have this ginormous (almost 2 GB) of things to read. So what did I do instead of reading? I uninstalled the app and the bookmarklet.