I thought that the Special Stage, Clubman Stage, and Tokyo Expressway courses all take inspiration from various Japanese highways already. (Sans SS Route X, being set in the USA.) Between these and the actual layouts of these highways, I think the big thing that I'd prioritize, in any track design based around Japanese highways, would be to have a good track width. Those other three locales can feel quite narrow, although I do love both layouts of Tokyo Expressway South. But it feels like the other locales (including Tokyo Expressway East & Central) limit themselves to ideally accommodating lower classes of cars - though I think that can still be fine. With this in mind, I think all these designs could still stay in the series, but get slight redesigns much like an actual circuit does, such as potentially adding more run-off areas, or removing some of the barriers to widen the track. (EDIT: Now that I see you've mentioned R246, I think that's one course that could also use some more of those sorts of modifications.)
For all tracks in general, I would especially add a "suggested option" listing for each track layout, and it'd include metrics like the preferred maximum amount of cars, and the strongest class (and/or Gr.X cars) that'd be ideal to use on the course. It wouldn't prevent you from doing something outside those metrics if you wanted (e.g. Gr.1 @ Tsukuba), but it'd be more of a guide. I consider this not unlike how you can get a tourism book on the best restaurants in a town, but nothing will stop you from just going to the local McDonald's if you truly want to.
EDIT: We also should consider that it would appear that many of the Special Stage courses may have a potential to be merged (or otherwise recombined) into a broader complex, including Route 7 from the PS3-era games. I recall that there were some exit ramp signs indicating directions to other layouts, as well as off-circuit sections of at least one Special Stage course being available to be driven on, via hacking.