There is a big difference between Ryza and the other two. Up until Ryza came out, the games used a traditional turn based battle system. With Ryza, they introduced action elements into the gameplay.

Personally, I'd recommend the later. Atelier, to me, is mostly about the crafting. I want to abuse the crafting system, which is somewhat different in each sub-series, to create gear so strong I basically don't have to think about combat. With the new system, once you achieve that, battles are a lot faster. But it's fun too, not just faster.

Other than that, you can take whichever you feel like. I haven't played an Atelier I didn't enjoy. They all have enjoyable characters. Keep in mind, the early games have time limits. I don't quite remember if Sophie or Ayesha have them, but Ryza doesn't.

Oh and I've heard the newest one is quite weak. But you didn't mention it anyway. Apparently they gutted the crafting...