In all board games I played that include 3D figures (plastic, metal etc.) the figures itself can be easily changed to flat cardboard tokens.
My questions is do you know any games in which the actual shape, orientation and modules of it play more significant role than just a token?
HeroScape is a miniature game where the battleground had complex 3D terrain. Line of sight was determined by where in the miniature the "eye" was.
The Knights of Catan expansion of Settlers of Catan uses Knights with variable equipment, which is stacked onto the knight figures.
Lemming Mafia keeps track of how many cement shoes a lemming has by putting gray pieces into the figure's bottom.
Coppit works by stacking tokens, easily up to 10 high. This would be much harder with paper or cardboard tokens.
Tactix uses dice and their orientation on the board as figures.
In most cases, you could replace the figures with card board tokens, and e.g., switch out a token for another, or pile on tokens.
Figures have some advantages over cardboard tokens:
they are easier to pick up and move
they have a better look & feel, and with that the whole game looks like it's higher quality
if the game board is tight for space, tokens can easily slide to adjacent fields (especially when piled up), where figures are less likely to move
token towers are likely to fall over when stacked too high
