Addressing some of your questions which haven't already been answered...
MD2s are slightly faster. That, and the ability to do arbitrary morphing animation, are the only two reasons to use MD2 that I know of. In every other way (including the most important point, quality of visual appearance) b3d is far superior.
MD2 does not support a second UV set.
Bones are useful for many things besides just runtime animation. For example they are generally useful for keeping track of positions of body parts. You can easily attach weapons (just parent the gun to the hand bone,) do hit location (determine which part of the body was shot,) etc.
MD2s are slightly faster. That, and the ability to do arbitrary morphing animation, are the only two reasons to use MD2 that I know of. In every other way (including the most important point, quality of visual appearance) b3d is far superior.
MD2 does not support a second UV set.
Bones are useful for many things besides just runtime animation. For example they are generally useful for keeping track of positions of body parts. You can easily attach weapons (just parent the gun to the hand bone,) do hit location (determine which part of the body was shot,) etc.