If the issue is not shooting in general, but Empire shooting (and at that, Handgunners and Crossbows), then a simple change for Empire would be in order. Like others have said, making them cheap could help, but it is more likely people will go "Awesome, 25 more points to spend." You could steal rules from the Imperial Guard to represent the regimented tactics of the Empire.
First Row Fire, Second Row Fire
If a leadership test is passed, the unit may fire twice in a single shooting phase. The unit must fire at the same unit, but are treated as separate actions for all other purposes. May not be used in the same phase as Take Aim, Fire.
Take Aim, Fire
If a leadership test is passed, the unit has +1 to hit for that phase. May not be used in the same phase as First Row Fire, Second Row Fire.
These would show how the Empire are meant to be the only professional army, whilst still being human. The leadership test represents the fact that it is training and something you cannot 100% rely upon. Although, it all depends on how much else changes in the book.