Probably already mentioned but flexible unit size would make life much easier. Reduce the minimum size for certain units (like from 10 to 5) and implement the possibility of adding individual minis. I know the understrength concept is to sell more minis, but the whole unit size restrictions are particularly annoying (like, I'd be ace to field my 8 dryads for 96 points).
I'd also make some changes to army building, as the previous point could lead to battleline tax abuse. So instead of +2, 0-1, etc... I'd go back to percentages. I think they help to balance army compositions instead of min-maxing everything to fit as much as possible on heroes, behemoths, etc...
Last point, prevent units from shooting when engaged in cc and add some form of friendly-fire. It makes sense from a logical point of view and would tone down the shooting domination. Possibly adjust point cost of certain units.