have you converted the characters to the 'game base' version? For a webgl or mobile app the full skeleton will be pretty heavy.
You can also 'optimize and decimate' the characters before outputting them. This would let you lower the poly count etc. Also when you export, are you using the instalod options to bake the texture atlas etc?
Character Creator provides quite a few options for optimizing the characters...
not sure about restricting morph targets that are output though...
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