As shield cancel isn't an intended mechanic in SK, but to fix it seems that it would be hard, I thought about a way to work around this, at least in the Antigua line.
Do you know how when using the charge attack in the Antigua lines, a bird appears (Depending on path)? Well, we would put a smaller "bird shot" in the last shot of the clip, that would do increased damage.
This way, we would make more attractive the idea of using the full clip, or at least give it a deeper mechanic. Maybe this could be implemented in other weaponry somehow.
Where is it stated by any of the developers that it was unintentional? I'm not accusing you of misinforming or being presumptuous, just asking for a citation since I don't happen to remember such a thing and doubt that most readers do.
Also, unintentional does not mean undesirable; see _serendipity._ It is of importance here, though, in light of the non-Pierce Autoguns...
Shield-cancel has become an important part of SK gameplay, whether it was intentional or not, and I can't recall any evidence that it is in any way problematic on a global level; the relative balance between toothpicks and other swords is screwy, but front-loading rather than back-loading the attack combo is only one small part of why. I do like your idea of more back-loading, though, for the same reason of depth you described. Moar nuance is good, a sense of meaningful choice is a big part of a satisfying game experience for most peops.