The aptitude system is unbalanced. This has been mentioned a couple of times by now, no one disagrees.
The flawed system is a problem for NEW players, because it adds work to the GM who has to come up solutions to make it fun for everyone, i.e. minimize the consequences of game-mechanical imbalances between the players. This might be easy for experienced GMs, but it is hard for new GMs.
However, Dark Heresy is full of archetypes so we do need a system to guide new players in terms of how to nudge them in the right direction given the archetype they are playing. In other words simply scrapping the system is detrimental for new players.
So I think that FFG should give the aptitude system some more thought. Realistically the imbalance could be solved simply by having new DH2 books working actively on improving the balance between the aptitudes. Maybe a few errata changes are needed too.