Yes by adding a clock crystal that matches the Game Boy's. A link port can also be added.
Cyclone IV handbook says the EP4CE15E17C8N has 15,048 LEs, 594 Kbit embedded memory, 66 18x18 embedded multipliers, 4 general-purpose PLLs, 20 global clock networks, 8 user I/O banks, and 343 maximum user I/Os in the EP4CE15 series but 256 pins on this version. As a 1.2V version (not low-power), it has a top clock speed of 166MHz; timing issues will apply, but the Gameboy is 4.194304MHz, and the GBC 8.388608MHz (twice GB).
The FPGA allows M, N, and C counters from 1 to 512. The PLL multiplies the clock by M/(N*post-scale counter). I see an A510N, which is a 32.768MHz oscillator. For GBC, you'd need to multiply by 1/0.256, or 1000/256, so use 125/32. For Gameboy, use 125/64. Divide these by 2 for the PPU clock and 4 for the CPU clock (if you need PLLs, just produce the PPU clock in the first place, and divide it by 2 for the CPU clock). Gameboy Advance clock is twice the GBC clock, but it uses a superscalar ARM processor and implementing that is difficult (and might cause timing issues, requiring slower clock speeds, although the FPGA can probably handle it), plus the FPGA may not have enough LEs.
SD2SNES also has a USB port, so you just need a USB-to-link-cable.
SD2SNES is open-source, so maybe start a kickstarter to pay someone to implement all this stuff. Should work on SD2SNES Pro but it's going to be as much of a lift as creating an FPGA Gameboy Color.
