What the AIA does is two-fold:
1) It changes the rule from "first to invent" to "first to file" when two inventors simultaneously seek a patent for the same invention;
2) It expands the "prior user rights" defense so that if you've been using a technology commercially for a year before the patent filing, you're not liable for infringement.
So if you weren't going to patent something, and keeping it as a trade secret instead, it's not clear that under AIA you have a new incentive to go patent it. If you weren't going to patent it anyway, there wasn't going to be a "dueling applications" situation, and "first to file" wasn't going to come into play anyway. And if you disclosed the technology instead of keeping it secret, then prior art comes into play and AIA expands the cases in which prior art can be used to invalidate a patent.
I'd personally like to see a merging of the "prior user rights" and "prior art" defenses. It should be possible to invalidate a patent by showing that someone else was using the technology before the patent was filed, even if that other person didn't publish.
Of course, one way to achieve that effect under current rules is to publish instead of keeping technology secret. If the tech community is really opposed to patents, especially software patents, then it should take additional measures to publish exactly how all their technologies work. This is something Google, etc, can take the lead on without waiting for legislation. Establish a rich database of prior art that can be used to invalidate future patents.
How is the patent office going to manage the increase? It's not, the system is going to slow down even further.
This also increases the cost of innovation. If I have a business, invent something, and don't patent it - I'm screwed regardless of if I prove I created it three years prior to the filing. In other words, now you have to file patents for everything to protect your ass (because it's not good enough to be able to prove you invented it first X years ago), and that's a very expensive proposition, particularly for small companies. This encourages the patenting of every little detail possible, even more so than today. Because if you don't patent every little detail, now you will have no right to self defense on the basis that you were the original inventor - they can come after you for every rounded corner you failed to patent, so to speak.
This forces everybody into the patent game.
The rationalizations being offered up, such as that this will be good because it forces openness on innovation are not only wrong (all it actually does it make it easier to steal technology for countries that already don't respect foreign patents), but the negatives are going to far outweigh any supposed benefits.
In five years everybody here is going to be complaining about how they really botched this piece of legislation and how it created more problems than the old system. This will turn out to be an extraordinarily expensive and destructive change; it is not the right approach.