Just some more of my thoughts on the topic.
1. Even with a Japanese ROM, making the polygon characters function like their base form would be difficult. The most obvious examples are Polygon Yoshi (doesn't have the egg shield) and Polygon Kirby (swallowing).
No doubt about that.
2. It would be used as you describe for balancing the cast instead of acting as a way to play the Japanese version of the game. This encourages the attitude "my character isn't good enough which is why I'm not winning." Just wait until you get bodied by a Samus and then you'll understand.
Have you ever seen a Samus winning a Major/National? Japanese players doesn't count.
Either way it is still enjoyable. Since you could play the japanese version of whatever character. Although some characters like DK don't change at all in japanese, It could work as a PM-esque character balance and would create interesting matchups, although this only would affect low tiers. Anyways, just like the original polygons and the "new" stages layout, if people don't like them. They may choose to ignore it. I was always wondering how much this would affect the meta or the matchup chart.
On a side note I think this would be the most balanced lineup and would be interesting to play and test those matchups.
Pikachu (U)
Kirby (U)
Falcon (U)
Fox (U)
Yoshi (U)
Jigglypuff (U)
Mario (U)
Samus (J)
Donkey Kong (?)
Ness (U)
Link (J) with (U) buffs.
Luigi (J)
3. I don't want to. This sounds selfish but you have to realize modding is very difficult. When I seek out large projects or ideas, I do it because I know my (and in this case, the work of Fray and PGC), will be worth the time and hard work. The first step of enabling polygon specials took me roughly ~20 hours of research and brainstorming not including the time looking at DMA. Actually implementing the specials takes another hour or so per character (which is why only Mario and Fox work right now) before any sort of changes occurs. I couldn't imagine spending that much time to enable characters that won't play identically to the Japanese version (think hitlag on drills, di, etc.) either way.
This seems more like a practical limitation, rather than being selfish. It is understandable.
4. One of the most common things fans of 19XXTE thanks me for besides the mod in general is the revival or longevity the features add. Some of the hacks keep people playing and potentially attract more people to the game. Japanese characters don't do that.
Are you sure? Any feature that could be implemented to add variety in the game brings more longevity, because we are playing a game that has been around 17 years and anything that could be added helps refresh the game like new. Yeah, I know, the Japanese stuff doesn't make much sense for the American player. But think it. Everyone plays this game. You make happy a lot of people with each new feature added. It just would become a less boring experience since it helps relieve the fact we are playing the same over and over again. But thanks to the improvements made, this hack always brings something to keep on playing.
In conclusion, rather than a thing of preference or potential game/meta breaker, or region, whatever. Realistically what limit this idea is the fact of the high difficulty of achievement to fully implement it. That being said.