That's the Cypress FX2LP USB microcontroller (I recognize it because I use it myself). If you're using the Hi-Speed USB transceiver, then you should really go with a 4-layer board. Without that ground plane right below the top layer, it will be near impossible to get the 90 ohm differential impedance that you want for the USB D+/D- lines.
http://www.cypress.com/?id=4&rID=34128 flat out states that 4 layers is required. It also states that controlled impedance is required, but in my experience you can usually get away without it, so long as you carefully research your fab's typical stack-up and work out the right width, space, and height.
http://www.cypress.com/?docID=25406 also provides more info on calculating the width, space, and height for the D+ and D- lines.
4-layers isn't that much more expensive; Advanced Circuits has a 66 each deal for 4 layer boards that I use quite often for projects that use that very chip, as opposed to the 33 each deal for 2 layers.
In regards to your actual question...use plenty of bypass caps, as close to the pins as possible. If you split the bottom layer to have VCC and GND, don't have a trace cross the split on the top layer. Keep all high-speed signals on the top layer because the via inductance can kill what fragile signal integrity a 2-layer board has.
You will hate yourself if you do stack up number two ;) Maybe that's harsh but it's a going to be a PITA reworking a board with all internal signals. Don't be afraid of vias either.
Let's address some of your questions:
1.Signal layers are adjacent to ground planes.
Stop thinking about ground planes, and think more about reference planes. A signal running over a reference plane, whose voltage happens to be at VCC will still return over that reference plane. So the argument that somehow having your signal run over GND and not VCC is better is basically invalid.
2.Signal layers are tightly coupled (close) to their adjacent planes.
See number one I think the misunderstanding about only GND planes offering a return path leads to this misconception. What you want to do is keep your signals close to their reference planes, and at a constant correct impedance...
3.The ground planes can act as shields for the inner signal layers. (I think this requires stitching ??)
Yeah you could try to make a cage like this I guess, for your board you'll get better results keeping your trace to plane height as low as possible.
4.Multiple ground planes lower the ground (reference plane) impedance of the board and reduce the common-mode radiation. (don't really understand this one)
I think you've taken this to mean the more gnd planes I have the better, which is not really the case. This sounds like a broken rule of thumb to me.
My recommendation for your board based only on what you've told me is to do the following:
Signal Layer
(thin maybe 4-5mil FR4)
GND
(main FR-4 thickness, maybe 52 mil more or less depending on your final thickness)
VCC
(thin maybe 4-5mil FR4)
Signal Layer
Make sure you decouple properly.
Then if you really want to get into this go to amazon and buy either Dr Johnson's Highspeed digital design a handbook of black magic, or maybe Eric Bogatin's Signal and Power integrity Simplified. Read it love, live it :) Their websites have great information as well.
Good Luck!
Best Answer
I ended up changing the layer type to conductor and changing the plane shape to dynamic copper and it worked. There was clearance around the vias for thelayers they were not attached too.