C) armor is broken far too easily by enemies
You should work on reading comprehension, cause that's contained within A, and it is not entirely true.
During my play-through, It was only in a few fights that any of my characters had their armor depleted, and once I got the relevant skills to refill it, it was rarely a problem I couldn't work around of.
It's also not a problem with the mechanics, nor one that would be solved by merging the skill points being spent.
It is entirely an issue with tuning the existing system, which isn't really going to be a sufficient solution anyway.