The stuttering is caused when we upload new textures or 3d models from the CPU side to the GPU. We have done our best to make this as smooth as possible, but we can't go below a certain limit.
If Aerofly runs at lets say 100 FPS, one frame takes 10 ms. However when uploading a texture to the 3D card, the driver has to stop for a tiny amount of time, grab the texture from the main memory and upload it to the GPU memory. As a rough estimate, this can take as long as 25 ms. So at that point the 100 FPS is interrupted for a small amount of time and you notice this as stuttering.
As modern OpenGL drivers improve, we might be able to reduce this stuttering, but it can't be completely eliminated.