When it comes down to it, PO and Showdown are mostly personal preference. A lot of people loathe Smogon's community so Pokemon Online is the general alternative. PO and Smogon run different tiers as well as having different interfaces of course. It's easier to implement new theoretical meta-games on Showdown though compared to PO from what I know like CAPs and stuff that changes battle mechanics (STABmons yay!). Reborn has had a PO server for years so that's where most of the community reside, but I know most head to Showdown for laddering including myself.
There is Pokebattle, which is pretty interesting. Basically all Pokemon are assigned points and you have a limited number of points to build a team with. It's apparently in public beta, I haven't tried it yet though.