Difference between 128 bit 250 MHz and 256 bit 125 MHz

Both can be taken care in my FPGA. Question is when the data path has changed and it is changing architecture(i assume as the files are totally different), there will be some change in the performance also.

In short, when I change my data path width to 256 bit, what all are changed? I want a 256 bit data path but my PCIe is unable to boot with it. In my 128 bit 250 MHz, my kernel boots and SSD is detected.