Let me preface this post by saying: I hate kill points. Here are some thoughts I have on the different ways to run a Annihilation mission in a tournament format.
First of there are the two common scoring methods for Annihilation:
Kill points took all the hard math(you know: addition and division) out of determining the winner in annihilation missions. Everyone knows the common example of why KP are a problem: that a 260 point Land Raider scores you the same amount of points as a 35 point Rhino. A common argument I hear for KP's are that they balance Small Model Count(SMC) armies against Multiple Small Unit(MSU) armies. I think it overcompensates for MSU's advantage in objective games. SMC armies tend to have halve the available KPs as MSU, and the MSU KPs are much easier to claim.
The old tried and true method for kill-em-all scenarios. It has the advantage of providing fine granularity that KPs don't, but can be a hassle to calculate when 50% casualties come into play. Plus they can be hard on armies that have a small number of expensive targets. This is really hard on the small model count armies, flipping the polarities on the way KP's reward small armies and hurts MSU. Victory points reinforce the advantage that MSU has in objective games, which is not necessarily a good thing. One lucky shot in this situation can swing the score several hundred points.
I have an alternate option that I would like to test out in future tournaments:
Graduated Kill Points
This option gives kill points a little more granularity. Basically a unit is worth 1 kill point for every 100 points it's worth. 1-100 points is 1 KP, 101-200 is worth 2, 201-300 is worth 3, ext. ext. This rewards a player for taking out a hard target in the same way as VPs, while still being fairly abstract like KPs. For instance a Land Raider(260 points) and a 10 man Marine Squad with Rhino(205 points) are both 3 Kill Points. As a bonus, the Marine player doesn't get penalized for using combat squads. Broken down the rhino and two combat squads are 1 KP each. This approach allows the SMC armies to claim easy kill points while the MSU armies don't have to dig themselves out of a huge KP disadvantage. In this system available KPs for MSU armies should roughly stay the same. KP's for the SMC armies should go up, but should stay lower than the MSU lists. For instance, take 4 units at 70 points each. This counts as 4 KPs in this system and cost 280 points. A single 280 point MC in another army would only count as 3 Kill Points. You still maintain a slight edge in annihilation for running SMC, but it's not as drastic of an advantage.