Thats assuming the FPGA is actually capable of being clocked over 33MHz.
To keep costs down there is an extremely good chance that it is *not* capable of being clocked faster - otherwise it would *already* be at 66/133/whatever zillion MHz.(Why put a nice expensive chip in your box if you're going to underutilize it).
To get a faster PCI bus you're probably talking chip or motherboard swapouts. And, to be frank, the Omega motherboard is already quite out of date in terms of hardware (Hint: SDRAM is obsolete.).
Your points on compatibility are also pushing it. Exactly the same is true for the Omega and it's "different" hardwares. And please, don't try the argument about how the FPGA can magically be repogrammed to solve all our problems,