Atomos isn't very good, but it does have its uses at least, which is more than I can say for Cait Sith.
The shuriken thing is a really nice addition for Ninja, with one problem: They added a bunch of new shuriken and they all have really bad base damage (less than daggers, the level 106 or whatever shuriken actually has less damage than the level 80 one, because back before level cap they were still making shurikens with really high base damage).
I think the best thing that's happened to XI in the last year and a half or so is that the game is more "playable" than ever, with summonable NPC partners and lots of old content that can be solo'd or low-manned that still retain some relevance. It isn't like those really early days where people will sit in town waiting for a party, there will pretty much always be something to do if you look for it. They also added a lot of incredibly long-desired conveniences like armor sets that can be macro'd, locking your appearance, checking your accuracy, and home points in many popular areas that you can warp between.
The main complaint from long-time players is the lack of large-scale content for groups, but since I don't really tend to do that sort of thing it doesn't bother me as much. I've always been more of the 3-8 players or so sort of guy with this game.
The story has been ramping up somewhat, but given how long it takes for them to release a story patch
I'm guessing there's still going to be like half a year or something before they finish it. Seems like according to the latest announcements from Matsui, the Adoulin Missions will reach their conclusion in November. Looks like you'll be playing again sooner than I thought, Ramza.