The question is: What is 3D anyway?
There are games which are completely 2D, like (original) Donkey Kong.
There are games which are completely 3D, which you play in Virtual Reality.
And there is a whole lot of gray area between those two - if you go back in time, many, many games claimed to be "3D", for different reasons. Isometric Perspective was surely called 3D when it first came out. Wolfenstein 3D takes place in a 2D environment, rendered in a way to simulate perspective. Likewise, New Super Mario Bros. uses 3D models for graphics, but is still a 2D sidescroller. Is it more 3D than Donkey Kong Country, which used prerendered models which were originally 3D, but put into the game as rasterized sprites? Donkey Kong Country Returns is a 2D sidescroller as well - except this time, there are not only 3D models, but also changes in perspective, making the world seem more three-dimensional, even though it's more like a 2D surface bent in space.
On the other hand, there are games like dwarf fortress, which take place in a three-dimensional world, presented in 2D (layer by layer).
Both arguements DrSuperGood makes are not that clear-cut. The whole z-height-deal is shared by many games considered 3D, eg. Cities Skylines. The whole landscape is just a plane with bumpmap. There is even a program called z-brush, which uses the same concept to create 3D models. Quake, the first (?) game to feature what is understood as 3D, did not need a GPU, so if it's 3D, it's completely in software.
I don't want to claim Simutrans is a 3D game, just that there are a lot of numbers between 2 and 3 and no clear-cut definition which is which.