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There's also the option of sitting down with the player and explaining exactly what you just said.
"I can tell from the character you're describing that what you want to do is get into melee and be a big, deadly bruiser. However, the build you've described is so good at melee that I'm concerned that it's impossible to challenge your character without negating his entire concept. Let's look at some constructing some house rules and/or adjustments to your build so that we can all be happy."
Of course, it's also possible the player is looking to design an invulnerable, ultra-deadly blender of doom, and doesn't want to be challenged; I can't say, as I don't know the player. Maybe he wants to feel like he's steamrolling everything in his path.
Unfortunately, nobody, game designer or not, is perfect. Games like Pathfinder tend to break down as more and more material gets released, and players have more time than designers to invest in identifying rules synergies. I've put together a couple of very interesting builds in my time, often by combining a couple of relatively obscure rules sources that were never really intended to be used together (at least in the sense that they were designed without knowledge of each other).
Couple that with the increased complexity of high-level play itself, and yes, there's a lot of potential for the game to break down. The best solution I'm aware of is to look at what breaks the fun of the game for you and your group, and look into addressing those things, quite possibly by banning them.