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So let's say that FPGAs turn out to be a healthy and profitable substitution to GPUs as we hope, so far Cryptonight is the only algo that was able to put ASICs out of the game for a while, this being said, won't ASICs just be developed for the remaining algos, beating FPGAs at what they can do best?
If so this leaves me thinking that FPGAs profitable work could then be allocated to Cryptonight, which is ASIC resistant as we speak, but as you have stated yourselfthis algo implementation is not the best mining use case for FPGAs and at that point once more accessible FPGA mining solutions are released and more FPGA hardware is purchased won't that put us back where things are now?
Let me answer. All the answers to your questions - yes. But you can do a lot before these problems arise.
I think that ASIC miners will appear for all more or less good crypto-currencies that exist now. But until then, the FPGA will bring income of 100-200% for 1-2 years, it is quite real.
There are several ways to keep FPGA solution, inclding:
1. Adaptation to reality every 3...6 month by implementing a new algorithm.
2. Creating FPGA-solver, that is impossible to reproduce in ASIC more effectively, than in FPGA.
3. Creating of altcoin with POW function that would be usable in some real-life application (genome, networking, etc). See Amazon cloud instance F1 with Virtex Ultrascale+, it's price ~1 USD/h..
Speaking of current problems, it is much more simple to implement miners by using existing hardware. Ironically, people who have FPGA (and programming skills) do not trust in cryptocurrency and do not consider such activity. So we have a chance.