Why do you think this is a limitation?
If your character is in the middle of a running animation when it hits a wall, you want to show a different animation like stand/idle whithout a hard switch from one animation to the next animation.

You can blend the vertex animations from your current animations frame to the target animation to let it look like a smooth transition.

With ent_morph you can change the run.mdl to die.mdl if you want, but this would create a hard break in your animation.
I would only go this way if I have already a lot of assets created as separate animated models. Otherwise I would advise that your artist should change his workflow to create the best fitting export files for the selected game engine.
If he does not change his workflow, the developer has to create the functions to make the animations smooth.

If you work against the engines techniques, you create additional work for your developers.


[hint]
The second model should be preloaded in order to prevent harddisk access during your animation change.

You can use ent_morph to replace a green tree with a burned tree if you use some big explosions and fire.

I hope it helps a bit

-- slacer