B3D vs 3DS and X

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Yes b3d is the only format supported for boned animation which gives the best results visually but can be a bit slow due to its DirectX7 implementation. In DirectX7 the CPU needs to calculate vertex positions. With later versions of DirectX this caculation is done by the GPU which makes it a lot faster.
As mentioned the polycount and the number of bones will play a part. Vertex weighting can also slow down things by increasing the number of calculations required.
3DS or X format models can be used but only using segmented hierarchial mesh animation which is a lot faster and is great for mechanical type structures but not so great for humanoids as you can "see" the seams between segments.
A possible option, especially in an RTS type system for viewing the models from very high up etc, would be to use a mixture of both in a kind of LOD system where you could display the boned character when up close and the mesh animated model when far away.
For very far shots you could even go as far as creating 2d animated sprites from your 3d models.
Spriteforge does this very well and PaceMaker also has an option to creste 2d animstrips from your 3d models.