I think it's pretty clear they want to get all the iOS mobile devices on the fall timeline, which makes sense with iOS getting updated in the fall as well. Debut a new iOS and new iPhones, iPods and iPads along with it. Macs in the summer, and I'm betting on a TV-oriented spring, whether it's an actual Apple TV set or a more powerful Apple TV box. Plus, as far as engineering goes, it makes sense to get the iOS mobile devices released around the same time. They have a lot more in common internally than not, and now the chips can be refreshed on a more straightforward schedule.
In any event, I bought the iPad 3rd gen. on day one like I've bought every other iPad so far on day one, and while it irks me a little more right now that they're updating it earlier than usual, I get why they're doing it if only because of the switch to Lightning, but as said, I'd imagine that the iPad will be permanently refreshed in the fall. I don't expect a 5th generation iPad until next October at this point.
So, why the A6X? Well, the A5X is the weak spot on the iPad 3rd generation, clearly. If they're not going to update it again until next October, they needed to get that A6 chip in the thing sooner rather than later, so why not do that now when they also refresh it for the Lightning adapter? What else are they going to do in the near-future outside of bumping up the internals? The form factor will improve at some point, but I'd bet we're still a ways away from that.
Basically, if they were to just put this out in the Spring with the 4th generation specs, it'd be a disappointing upgrade, but as a product refresh, it's great. Now they have a year and a half between major releases to focus on a more dramatic overhaul if they indeed go that route.
So yeah, it's a little annoying right now, but I think long-term it's for the best. I think it'd have been far worse if the iPad was stuck on that A5X until next fall if they do indeed keep with a fall refresh moving forward.