I think you should find a good balance.
In general the fill rate is not a problem on the DC, but memory consumption for geometry is. Fill rate is a problem on the GCN and PS2 because they use rasterizer graphic pipelines, unlike the DC which uses a deferred tiled renderer (a raycaster), but they have much less of a storage problem for geometry due to more RAM. Transparent polygons on the DC are also cheaper than on the GCN/PS2.
Another reason why you might not push as many polygons on the DC in practice is that transforming and clipping geometry causes CPU overhead, while the GCN's GPU for example can take care of that due to T&L support. The DC CPU has some nice instructions for matrix math, but having a completely different processor work on that data in parallel is very beneficial.
The PS2 is a floating point math monster, but in practice it's quite difficult to get maximum performance out of it. Even AAA developers back then had serious issues getting even half the performance out of it (check out the Sony and Naughty Dog slides I mentioned before). It's much easier to get good performance out of the DC and GCN.
A game like Virtua Fighter 4 is very different to an open world RPG like Kingdom Hearts. You have very few meshes to store (2 high poly characters + relatively low poly background), you want high quality textures and don't need to swap stuff in and out of memory during runtime. This works well on the DC.
Now Kingdom Hearts doesn't look very "open world" to me (doesn't seem to load resources in the background etc), but in general you'd need a higher amount of RAM compared to the other game type to make swapping techniques work well enough (to have a buffer for reading from disc).
I think a bigger issue for KH2 on the DC would be disc storage space. GD-Roms only store about 1GB, DVDs about 4.7gb. That means you wouldn't be able to have as many prerendered cutscenes as in FFX. Disc reading speed is also important, which is probably higher on the PS2, but I'm not sure.
Here's a Shen Mue development post mortem from March this year, where the developer speaks about his challenges developing a real open world game for the DC: http://www.youtube.com/watch?v=Amu0_EunHmM
My libgl playground (not for production): https://bitbucket.org/bogglez/libgl15
My lxdream fork (with some small fixes): https://bitbucket.org/bogglez/lxdream