So, what are the main technical differences ?
Do they offer the same functionality ?
Are they meant to cover the same area of use ?
Price difference ?
Production difference ? (Handmade / Machine made)
What can A do that B does not ?
They're very different:
FPGA Arcade will offer 68030 to 68040 level performance depending how much performance they manage to squeeze out of the TG68 core. Not sure about the softcore performance on the Natami, but the (optional) CPU boards are 133MHz 68060's and I believe their aiming for higher performance with the softcore when its ready/integrated (better/wider memory interface, more work per clock etc.). The Natami also seems to have a far faster memory interface that'll completely crush any classic and leave the FPGA Arcade in the dust too if they manage to make full use of it.
Functionality wise, they're similar though there are lots of small differences other than that the Natami has lots more memory (512MB on the board vs. 64MB I think for the FPGA Arcade), "SuperAGA" - lots of new screen modes, massively faster blitter etc. and they're talking about other enhancements such as extra coppers etc., while FPGA Arcade is AGA with possibly some smaller extensions (higher resolution, chunky modes etc. - whatever yaqcube manages to squeeze into the smaller FPGA).
FPGA Arcade isn't Amiga specific, though - there'll be C64 cores, Atari cores and a bunch of others, while the Natami is aimed squarely at being a modernized Amiga.
Price estimates of the FPGA Arcade is in the 200 euro range (+/-), while I don't know the price the Natami will end up at (they don't know for sure either, though I'm sure they have a better idea than me, but they're holding off on announcing a price until they know spot prices for the components when ordering). I'd be surprised if it ends up lower than the 600 euro range, though, given the complexity and the size/cost of the FPGA's chosen etc.
Basically, I'd consider FPGA Arcade as a heavily upgraded Minimig replacement that could also likely take the place of a not-that-heavily-expanded A1200 level machine + offer ability to use with other cores, while the Natami is offering performance and features beyond most heavily expanded classics with the exception of lack of PPC expansions (so far anyway - it has the expansion slot they use for the current 68060 boards).