The downside of a short scale is the tone. It just doesn't "measure up". Compared to say my 35" Modulus 6 a short scale is dull, weak, floppy and doesn't cut.
What short scale were you playing? I played a used Modulus at guitar center and it was horrible. The action was terrible. The tone was lousy. It really didn't measure up to the new Fender Mustang and Gibson SG that were hanging next to it.
As you can tell, I don't believe in blanket statements about the tone of short scales. That would be discrediting the whole concept behind Landing, Birdsong and Paul McCartney for that matter.