[NotQuantum]

One of the biggest issues is complexity. Sure you can make some fairly complex things within an FPGA fabric, like a CPU or GPU. However, you'll see a slow down in two areas. The first is routing, whereas an IC would just have a wire between two components, FGPAs have to route further and through different interchanges. Second, components can only be built up through the basic components of the FGPA, typically a LUT and FFs. The more complex components, the more small parts. Another aspect is memory; blockram works decent but it's an explicit design choice, DRAM via DMA is also a pain too.