Well, I imagine by now you’ve likely already decided (and probably have already completed, or not, whatever game you chose :-) ), but in case you haven’t or for anyone else who comes here looking for an answer, I thought I’d provide a few links to some useful (or at least I found them to be useful) discussion on where to start with the Atelier series.
There are these 3 conversations (one, two, three) on the Atelier subreddit, all centered around which of the 4-6 Atelier games (4 on the Vita, 6 on the PS3) to start with, with the third of those wondering about which is more laid back and less restrained (since many of the games have a time limit of sorts to deal with). Obviously the standard grain of salt, your mileage may vary, and to each their own all apply here, but as I said, it helped me at least put all of the games in context with one another.
Me? Well, I bought Totori Plus on the Vita during 2014’s Golden Week sale, but only played maybe 30 minutes of it before something else got my attention. However, for some reason I impulse-bought Ayesha Plus during this most recent sale, and am about 10 hours in, and have found myself really enjoying it so far. I’m using a walkthrough on GameFAQs, but I find that it doesn’t detract from my enjoyment of the game; rather it helps mitigate any stress I might feel from the time limit. Plus my understanding is that this game is the first in the Dusk trilogy, so if it really works for me, I can seek out the other two games in the trilogy, or move over to the Arland trilogy and play those.
Anyway, hope this helps duder!