Hating power play?
What if the player uses the system to get a solid, cohesive idea of what they want their concept to be, and happen to choose one of the more effective ways, numerically, to do the character's goals?
For example, the concept I had would likely involve lots of high level skill checks, and as little actual combat and dungeon crawls as possible.
"Powergaming" and "Making a concept and sticking to it" are not mutually exclusive. In fact, they aren't really related at all .
So what if my socialite can start, at the beginning of the game, with an effective 91 Charm if he is talking to other nobles from the bridge of his ship?? So what if my Techpriest can have an effective 92 on Tech Use checks, IF he uses the Library on the ship and IF he is taking his time to use his Foresight?
Those things can most definitely be a core part of a character's personality! "Savant level capabilities in tech use, and an obsession over technology" can be a core concept of a character, as well as "Very sociable and charming, makes people around him feel relaxed, and feels especially at ease when at the helm of his ship" can be another core concept for a character.
Also, it should be noted? That getting the numbers this high generally requires stacking bonuses. Bonuses which won't be available in many situations, and which only work when the character can usually take their time and function in their area of comfort and with their best tools, and maybe go through some rituals appropriate to the task at hand (say, showing someone around the swank parts of their ship, or do a bit of meditating and planning before they start work on the technological whatsit).
A campaign to find an intact and fully functional STC System is a valid quest for W40k.