Prototyping with the 'Adobe Suite' has the advantage of:
- pixel perfect shiny-ness.
The disadvantage is:
- pixel perfect shiny-ness.
The reason "AAA" companies use it has a lot to do with tradition in that that's what everyone used pre-internet. The big ad and design firms were never ones to jump on change so have slowly drug the Adobe Suite along with them.
This isn't all bad, of course, as it is now a de-facto standards, so there are advantages to that...files are easily shared between firms, clients, vendors and the like.
But it's also an incredibly heavy way to manage files. PSDs are not easy to maintain. DreamWeaver doesn't make useable markup. Integration between Adobe apps is nice, but also complicates workflows.
And the biggest challenge is that using something like Photoshop and Fireworks encourages designers to make 'pixel perfect' mock-ups. And that can usually cause as many problems as it solves...namely that that final developer product rarely will look like the original PSD for a whole host of reasons, and if not managed well, that can lead to client frustration (not to mention developer and designer frustration).
So, long story, short: The big advantage a lot of tools have over the Adobe Suite for prototyping is that they aren't dependent on heavy, high-fidelity files.
I'm presently working on a project where we're mocking up an iPhone app using PhotoShop. It's 'OK' for the first 10 or so screens, but now we're pushing 100+ screens and it's plain silly. You can't easily update 100 PSD files every time a tweak is made to some standard. Not that you should ever mock up 100 screens to begin with, but had these remained as more wireframes in a more agile tool, at least iterative changes would be a bit saner to deal with.