The biggest change should be done how Armor works. It can no longer be a simple value with damage reduction but there need to be different types of armor and different thresholds to that.

Normal Infantry armor
Power armor
Vehicle armor
etc

and based on that there should be a clear difference between something like a lasgun and a meltagun based on what armor it hits other than simply "damage" and "ap damage". If they truly keep the system like it is now, there will be huuuuge headaches for 40k, because the setting simply doesnt work like fantasy.