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for me it is clear that you have these problems
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I don't think, it's that simple. I have designed a number of two layer PCB FPGA boards with ACEX1K, Cyclone and Cyclone II, mostly prototypes, but also a small production board, that's manufactured since five years, and I had never problems of the said kind. Also forum members have presented surprizingly simple boards, that have been finally working. The present board has possibly more problems due to additional flaws, e.g. missing supply bypassing and a too light ground net. I would expect JTAG to respond though, at worst showing errors with large bit streams, but still able to give a chip ID.
To avoid misunderstandings. I don't generally suggest to design two layer PCB with FPGA. I also see 4 layer as a minimum for PQFP/TQFP packages and 6 layers minimum for full populated BGA. And I know, that a design can fail due to a bad layout. But I don't see it as a plausible explanation for the configuration problems. If signal quality issues are actually causing the configuration problems, you would be able to measure it.
P.S.: How did you solder the FPGA?
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