I like Refined Storage a lot, it's very simple to get up and running.
AE2 though, has some very, very nice features.
The main thing though is to decide what's more important for you.
One of the things I like about RS is that it's very easy to get up and running and is fairly simple to expand, for most basic things it will suffice quite happily.
When you need to 'go large' though, the features of AE2 come in handy and make AE2 worth considering.
One of those things is the way crafting works, you can put a bunch of machines around a single AE2 autocrafter block and multiples of a crafted item can be done in parallel.
The crafting panel is terrific, One issue you find when RS builds get large is having to craft a pattern and then go find the block that's pointing at the right machine to load the pattern into. In AE2 you can do this from a console, which is nice if your AE2 crafting interfaces are a long way away from your terminal.
And, we all love the Soaryn drive (I think that's what it's called).
One of my goals in my current game will be to build a big data/AE2 centre.
And.. AE2 just looks awesome.
AE2 vs RS is not a binary choice, one is not better than the other, it comes down to what YOU want from your storage / crafting solution.
I think they are both terrific mods
-Wuffle!