VPs can be gamed just like killpoints. I remember figuring out little things in 4th ed on how to make it just that more difficult for my opponent to collect VPs.

Keep in mind that, while lots of weak units are at a disadvantage with scoring, MSU (multiple small unit) armies have a solid mathmatical advantage when it comes to shooting damage output and durability. Take a Driagowing army with 4-5 units vs a Razorback spam list, and while those 4-5 Paladin units will probably each kill a Razorback easily, they can only target a handful per turn, and they waste a lot more firepower doing it. The Razorspam list can then put one lascannon at a time into the Driago list, with much more efficiency of firepower.

To balance out the fact that MSU armies have a distinct firepower advantage, we have Killpoints. Running MSU means that you risk giving your opponent an easy(er) victory in one of the three mission types.