It depends on what you want from the cooler. If all you need is cooling and you don't care about stuff like design and so on, a good air cooler is all you need. The Noctua NH-D15 will beat most AIO water coolers without much trouble.
What AIO's do offer is saved space, better design and (possibly, although not always) less noise.
When you get into custop water cooling, it's nto worth it to make these argument anymore, because everyone knows it, but it doesn't matter, because LOOK AT IT!!! Custom loops are fun :D