Good job! If it was me, I would probable have gone with Cypress CX3...
Yes I thought of doing that as well. But there are few issues.
I wanted to have this camera as UVC so that I need not to implement any custom solution on PC side. As this camera only output raw and UVC does not support RAW. So if I would have gone with CX3. I need to implement a application on the PC side to convert from RAW to usable format. Then i would have also need to implement my solution for controlling camera exposure and gain.
Second problem was availability of development board, FX3 board costs just a fraction of what a CX3 board goes for. Making custom board was a somewhat hassle with BGA and stuff.
But one very significant advantage CX3 would have offered, MAX theoretical bandwidth is higher compare to FX3. As with FX3 it is limited by 100Mhz 32bit GPIF, while CX3 does have this bottle neck so can go higher up to what USB 3.0 Allows.
Regards