First, Congratulations yaqube for the AGA implementation!!
Oh and for the patience with the not-possible-sayers..

(68060/PA-7150 softcore with Hombre chipset next?

)
A quick look at fpgaarcade.com seems to suggest there's no DB23 connector for a floppydrive (250 kbit/s?).
BUT, if there's any wired 5V I/O one can just connect and change some code in the sources, synthesize ("compile") and should work. Because for an FPGA there's not really any dedicated "port" just loads of general I/O.
The connections seems to be:
MMC, HDMI, CVBS, S-Video, 2x PS/2, 2x Joystick.
130-pin expansion.
Debug232?, ?, VGA, 2x General I/O, Power
Any price indicators yet for the board?
As for what resolutions are possible, and other bitstream dependent applications. An DDR DRAM that is clocked at 200 MHz with an 16-bit width will give 6,4 Gbit/s ; For comparision an 68040@25 MHz will consume 0,8 Gbit/s ; video 1920x1080@60 fps 24 bpp = 3,0 Gbit/s ; audio 192 kHz 24 bit 6 channels = 0,03 Gbit/s ; ZorroIII = 1,2 Gbit/s ; PCI32/33 = 1,1 Gbit/s ; Ethernet 1G well.. = 1 Gbit/s

There are some delays for each row switch and cas latency to take into account but with proper caching this will not be a problem. Good predictions on what memory sections that are worthwhile to cache will win performance points. Special care has to be taken for bitstreams that can't take disruption gracefully like video and audio. I hope the CPU and Ethernet etc.. don't mind waiting.
DDR2 have the same amount of transfers per clock cycle as DDR1. And DDR3 have very long latencies from command given to data in/out, and very special electrical interfacing (same for DDR2). To counter this sub 2 ns clocks are possible (ie FAST). So for any Amiga project DDR1 makes the best pain/performance choice. If the 2,5 V and impedance matching causes problems SDR (1 transfer/clock) at 3,3 V could make a good choice.
(I saw the answer above now regarding the floppy drive
answer but still can't find it at fpgaarcade. However as said, it's easy to fix.)