There are a couple of things to keep in mind when building a tournament mission format. I think a lot of people get this wrong.
I'm going to hold the NOVA missions up as an example of what I'll call "Balance Through Drawability."
In the NOVA, the hardest mission to draw was Victory Points, but it could still be tied - in fact, to help prevent the biggest struggle for VP we made sure the round where it was primary was Dawn of War, so that alpha strike was largely inhibited. Once Alpha Strike is inhibited, well-designed lists faced off have the capacity to make the strategic choices regarding how well they stay covered and how much they overextend themselves to keep the VP total close, and within tie range. That said, this was the hardest to tie, and as a result - the weakest mission for a good balanced format.
You'll see why in a second ...
Let's take a look at Quarters next. A lot of players initially glanced at quarters and thought that it favored armies with lots of mobile fast units, so that they could shuffle numerous things into any given quarter at any given time. This is false, in playtest and design both. Quarters most favors someone using LARGE units that are more elite and can take a beating. Basically, the kind of units you'd see in a Kill Points Optimized or low Kill Point army. Why do I say this?
Well, for Quarters, the best place to live for the majority of the game is the center of the board, so that later on you can shuffle high value units to overwhelm quarters on the VP front even if said units get knocked below half. A Nob Biker unit, for example, may retain a greater than 400 point value even if under half strength in some situations, and so be able to prevent an opponent from effectively "spreading" his volume of mobility and safeguarding multiple quarters from late grab. This forces opponents to keep LARGER portions of their MSU armies in quarters, rather than spreading out, or forces them to risk danger by closing toward the middle of the board. In short, if you have units that retain extremely high value while guarding center and dishing out a beating you have an advantage in a Quarters mission.
For Objectives, MSU is rewarded - the more scoring troops units you have, and the more units to contest you have, the better off you are. Opposite of Quarters, though they "appear" similar ... in Objectives you want to be able to spread useful and durable "enough" units to the far corners, able to snag objectives in each quarter late, or contest late, while forcing your opponent's target priority all over the place ... they gain advantages against armies with too few units in this mission.
Both Quarters and Objectives can READILY be forced into a tie by a canny opponent, even if his army is not ideal for "guaranteeing" a win for the specific mission.
So what's the point of our approach then? By tiering your missions together every round, but rotating which is the INITIAL win condition, and doing your best to establish missions that advantage some armies but can be TIED by any (if well played), you get into a situation where you are more rewarding skill, tactics, and forethought ... and less rewarding "bad luck" for a match-up.
I'm not sure we've gotten this "right," yet, but we're close - we'll get closer. Ya'll should do the same. Consider as you're building your missions how they work; this is some of the thought behind why our missions are the way they are.