Noticing that a fair point was made regarding "Time" vs "Skill" with one or the other accounting for becoming system protector.
My suggestion is make the system Protector mechanics a Triumvirate of the following:
A. Time - This would include actually being in the system, doing random missions, how frequently you revisit the system, this particular aspect can actually decrease over time thus lowering your rank if you ignore it in a system long enough, etc
B. Skill - This would include Profieciencies gained in the system, Tarot missions considering those are more skill based imo, Cabal missions, Investigations, Priority missions, etc
C. Glory - This should be made one of the factors for system protector rankings, The Black Crusades from Chaos, Tyranids invasions, Orc Waaaaghs, and charging headlong into these elite type missions should account for the glory earned to boost a players system ranking.
NOTE: Failure in any of these will lead to loss of overall ranking in the specific system.
Failure is a real world thing and it happens all the time in 40K why not use it for once.
I believe that if you have all 3 of these in some fashion able to increase and decrease due to failure in missions, loss of imperial troops, resources, heresy, etc then the system protector mechanics would be far more interesting and less static. The boring one dimensional X number only increases is not the way to make players happy nor the recipe for a successful long term game. You of course could have many more than 3 aspects to determine system rankings.
Again just my 2 cents =)
"Venerate the Immortal Emperor"