> Also,before redesign all board, check what impedance should be for all lines
> (datasheets), go through simulation software what impedance is now. Check
> what was impedance on previous version of PCB that worked (go through
> simulation again). So, maybe you can just change thickness of prepag (if
> that is possible) that match previous version of PCB (if you have same
> design of ddr3/mcu).

 not a chance.  increasing the line thickness to 4mil increases the
impedance by something like 4%.  there's no way i can use anything
other than 1.2mm boards.  there's ABSOLUTELY no way i can go to 6
layer.  and the dielectric constant for 6mil board separation would
have to be reduced to something insane like 1.0 in order to claw back
the reduction in separation.

 this *has* to have been taken into account in the design of DDR3
drivers / receivers, that there would be circumstances where the
impedance is off like this.

I am not sure if we understand each other here. Impedance of your lines are not function of thickness of board and thickness of line but thickness of prepreg and thickens of line. so, if you have for example 4 layer board you have copper conductor, then substrate then copper conductors etc and all of this are i.e. 1.2 mm thick. But when you calculate impedance you take into consideration only layer that is below surface if you line is on top (and because most signal lines are on top of PCB, if lines are in the middle of PCB board there are different calculation).

example here (h- thickness of prepreg)
So, for thickness of your lines you need to match with thickens of prepreg to be able to meet certain impedance. it does not mean that your total PCB thickens must be changed, you can vary some other layers of preprag, there are number of options with producers of PCB. You have to tell them you need 12 layer board and my layer of prepreg must be so and so thick, what can you offer me... Maybe this is possible, maybe not.