Just to clear some things up.
The NatAmi board uses a Cyclone IV EP4CE40 device (currently). This has 39,600 LE (Flop + Logic element) and 1.134 MBit internal memory.
As explained several times before on the Natami forums and elsewhere, the EP4CE40 is only on the first handful of boards Thomas soldered together. This was because the actual FPGA we wanted to use (EP4CE55) was not available at the time and we wanted to start testing systems quickly. However, all new systems (the MX board on my desk here too) are using the EP4CE55 with 55,856 LE and 2,340 MBit memory. Expect it to be filled to the brim with logic...
So your points on affordability are even more valid, since the EP4CE55 is a bit more pricey
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Whats the point in it, when current Amiga graphic cards can out perform it ?
The main point is actually doing things the Amiga way in the design spirit of the original Amiga. While RTG graphics cards might have been a good solution for upgrading a system that never evolved because Commodore just couldn't manage it, they are still just PC graphics chips stuck to your Amiga with duct tape, software supported with ugly hacks.
Now we actually have the chance as hobbyists to rewrite a bit of history and make a proper implementation of truecolor chunky graphics as native Amiga graphics modes as well as extended planar modes. It might not mean much for the user who couldn't care less how his web browser is drawn as long as it is fast, but it sure means a lot for people who enjoy the Amiga design philosophy and want to code for Amiga just like back in the old days. The other day we had planar graphics in SXGA up and running, for example.
This is good news to hear from one of the Natami Team members! I hope that you (the team members working on Natami) will not wait until it is almost ready to release, as I wrote that releasing it now, or in the near future will have the advantage of getting some programmers to start coding apps and games that can take advantage of these newer SAGA features so that there are some SAGA compatible apps and games written before the Natami is available and when it is finally released, there will be some SAGA apps and games available to show off the newer capabilities.
The people who have expressed interest to code for the dev systems are already on the team. If you are interested, join us

Also, though I know that too many cooks can ruin the stew, it might be good for the Natami Development Team to accept ideas and discussion regarding adding new SAGA features from talented Amiga developers who are not on the Natami Dev. Team. The Natami Team members can choose to accept or reject any ideas they don't think are feasible, or don't create significant benefits compared to the amount of work or resources they require to implement. Outside developers and hardware technicians may also provide key information, coding, or ideas that will help the Natami Team to complete the work on SAGA faster.
This is what the Natami forums have been used for the last few years, in case you missed it (easy to do so among the distracting Thierry rants, perhaps...

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NT