Remove plywood floor before insulating attic?
I'm assuming that the floor of the attic is insulated, and the roof is not insulated at all. Do I have the right picture?

Options

A: Put insulation on top of the plywood.  This is straight forward, and can be done with soffet baffles at the edges, and half a day's work with an insulation blower.  You can choose between cellulose and fiberglass.  The former is environmentally more friendly, and usually cheaper, and not nearly as itchy.

B: Remove the plywood, and put insulation on the old insulation.

C: Insulate the rafter space.


Only insulate the existing web.
Make the rafter space deeper by adding 2x to the edges of the rafter.
Use a higher R-value insulation between the rafters.
Fasten foam board to the interior edges of the rafters, then cover. 


Tradeoffs on removing the plywood

You lose the potential storage space if you put insulation on top of the plywood.   (You said you're not interested in doing this, but anyone else who finds this answer may be.) Removing the plywood will be a big pain.  You also lose the support.  More than one person has stepped through the ceiling of the room below when missing a joist.

While plywood isn't a vapour barrier, is will be a limited air circulation barrier.  Normally when adding insulation, you want about twice as much on the cold side of such a barrier to keep the dewpoint on the correct (cold) side of the barrier.  Blown in insulation is cheap.

Tradeoffs on insulating the rafters.

This is far more time consuming.  You either are getting less insulation, having to make the rafters deeper, or working with foam, then protecting the foam from fire.  This may or may not be necessary depending on local building code and the particular foam product.  See http://msdssearch.dow.com/PublishedLiteratureDOWCOM/dh_0944/0901b80380944bea.pdf?filepath=styrofoam/pdfs/noreg/179-00011.pdf?filepath=styrofoam/pdfs/noreg/179-00011.pdf&amp;fromPage=GetDoc

You could do this by putting 2x4 on edge on the existing rafters. then insulate.  If the existing rafter is 2x8 (7.5") then adding 2x4 will give you 11 inches.  Fiberglass at R3.5/inch gives you R38.  If the floor is 2x6 and filled well it's about R20.  

The flip side of this is that you have the space as a either storage, or hobby room, or potential spare bedroom, with the addition of a folding attic stair.  This room is halfway between two insulation layers so it will tend to be warm in the summer, and cool in winter.  

As even a roughly developed storage area it may increase the value of your house.  You could consult a local realtor to find out.

You can also blow in insulation in the hollow of the 'A' so it could be R60 for that part of the roof.

Another possibility would be to use foam insulation.  Insulate the 2x6 truss elements with bats, then put up 2" foam boards, then drywall.  (Foam board MUST have a firebreak -- it releases cyanide when it burns)  This has the advantage of insulting the thermal bridge that the 2x6 has in the roof.