At least as far as the game is concerned “unfinished prototypes” are valid, even if the devs like to be very inconsistent with them (sometimes refusing them, sometimes adding completely fictional vehicles instead)
For Japan there’s interesting possibilities:
Mitsubishi's domestic FS-X (JF-210)


Mitsubishi’s entry for FS-X, winning the competition against the Kawasaki design and almost being produced, if it wasn’t for heavy political pressure from the US forcing the cancellation of the domestic design.
Instead, foreign aircraft were proposed, and ultimately Japan settled on joint development based on one of these foreign designs, General Dynamics SX-3. This would then become the F-2.
The radar arrays for the JF-210 were prototyped, as well as a wing structure. It was set to use two F404-GE-402 engines, but I’m not sure if any were bought before the cancellation.


Mitsubishi F-X 23DMU

The initial “proper” design for Japan’s 5th generation fighter program, and the closest it can get to an "armed X-2, as that was the testbed to go along with this project.
Notable progress on it includes prototyped XF9-1 engines and XVN3-1 3D TVC system.

Mitsubishi F-X 25DMU

Another one of the F-X DMU designs, this time quite a bit larger. This one featured dsitinctly angled elevators and swept wings, but also a completely new, larger main weapons bay.
However it also retained the side bay design from the previous designs, storing SRMs in weapons bays placed between the wing and fuselage, just in front of the landing gear.

The main weapons bay for this design was built and tested.

Yes, this means 24DMU was skipped, sadly I couldn’t find any physical prototype parts introduced with it, let alone unique and vehicle specific parts.
Mitsubishi F-X 26DMU

The final iteration of 5th gen F-X, and the place where all the prototyped technologies converge. The engines, radar, TVC and even main weapons bay converge in this design.
However it was also changed quite a lot, sporting a more conventional trapezoidal wing, non-angled elevators and side weapons bays set in the fuselage akin to an F-22.
It’s also commonly featured in this cool blue camo, which is a very unique and interesting choice.
The prototype here is significantly more vehicle specific, being the center fuselage of the aircraft (note the side weapons bays).

A radar and “stealth” radome was also developed for either 25DMU or 26DMU (it would’ve been the same either way) but since I don’t know when exactly that slots in so I’ll just mention it here to be safe.
Maybe since it’s all one (somewhat) linear development of the same project up to 26DMU, chances are only 26DMU counts as the final version of 5th gen F-X anyways.

This alongside the fact that all of the previous components like XF9-1 engines, XVN3-1 3D TVC and main weapons bay remained unchanged for 26DMU might just make this the only viable 5th gen F-X option for the game.
Also there's the completed prototype
