I did some tests using the following hardware to determine the performance increase:
X58 Motherboard
X99 Motherboard
SYBA / IOCREST SY-PEX40039 PCIe2.0 SATA3 card
Samsung 850 PRO 256GB SSD
PNY Optima 240GB SSD

Samsung SYBA / IOCREST SY-PEX40039 PCIe2.0 SATA3 850 PRO & PNY Optima SSD
Samsung SYBA / IOCREST SY-PEX40039 PCIe2.0 SATA3 850 PRO & PNY Optima SSD
Samsung 850 PRO & PNY Optima SSD
Samsung 850 PRO & PNY Optima SSD

Here are the benchmarks I promised of the SSDs and PEX40039 PCIe Sata3 card.
I did not get the card to work correctly while my system was set to RAID on the X58 system.
Seems to be a BIOS conflict. So these were done with RAID OFF.

ssd_raid_compare_x99_x59_ich10r

It seems the performance of the PEX-40039 on the X58 PCIe Slot could not outperform the native X99 SATA3 ports.
However, the PEX-40039 did outperform the native SATA2 ports on the X58.
Another thing to think about if using the PEX-40039 on the X58 i7-920 resulted in a 2% – 5% CPU load increase.
Where as there is 0% CPU load on the i7-5930K, and i7-920 when using native SATA ports

There is approx. 30% increase from (ICH10R) to (PEX-40039 X58 PCIe)
and then about 30% from (PEX-40039) to (X99 Native SATA)
So going from an X58 Motherboard to an X99 motherboard will give your SSD approx 50% 60% performance increase

Seq read on ICH10R SSD was 288MB/s
Seg read on X99 SSD was 530MB/s