The game part will still be fun, but you play VLR for its narrative first. Many of the plot twists are heavily reliant on 999 for both context and magnitude. This is, after all, a sequel. If possible, you would be doing yourself a favor experiencing 999 first. This game spoils its most significant twist if you play in reverse order, anyway.
Options for 999 are DS, iOS, and Youtube. The iOS port does not have gameplay, as I understand.
Go to Gamestop, buy a Steam card, and use it to purchase Ys Origin. You won't be disappointed. Ocean should not derail the train.
From what I've heard, Never played it yet or got it yet, is that the iOS port doesn't have any of the puzzles, but I think, more story in place of the puzzles, which makes it a pure visual novel, in which the interactions come from the points in the story where you make the choices that determine which branch of the story you go on.
Played Virtue's Last Reward first too. Waiting for my copy of 999 to get here. I really wish I would have played them in order :( But i still think I'll enjoy it. I'm gonna need something to calm me down until 3 comes out though >.<