As for the question of should it allow one to make bad choices in the name of flavour or characterization, of course it should! That said, with each new edition the design becomes finer-tuned and as a result "bad" choices have a greater negative impact; and that's a shame.
You call it bug, I call it "feature".
First off, there is a difference between powergaming/min-maxing and optimal builds. An optimal build is a fighter with a greatsword taking power attack and weapon specialization to get the most damage with his weapon. A Powergamer is one who thinks the best starting rogue build is Rog3/Ftr2/Guild Thief3. A character can be built to do his job without stringing out PrCs, using obscure feats, or adding a myriad of templates.
HOWEVER.
There is also sub-optimal builds as well. These are the ones where the build actively hurts YOUR ROLE IN THE TEAM (God, how 4e!). A cleric who channels negative energy is not an effective healer. If you say "we are getting are butts kicked, we need a healer" and another player creates THAT, your no better off a healer than you were before. Similarly, any rogue who doesn't have sufficient ranks in Search/Disable Device is going to fail at the trapfinder role, which is commonly the role given to rogues. IF you have another trapfinder character (or never, EVER, encounter a trap in a dungeon) than its OK to skimp. If your DM likes Goodman Game DCC's however, you've just made a sub-optimal character.
4e "fixes" that. You can't make a cleric that isn't good at healing. Even if you never select a healing power, you still have healing word to fall back on, and its a lot easier to use than channeling positive energy (even if your evil, you can use it too). Likewise, no rogue can be bad at "roguish" techniques, so you can disable traps with the best of them without blowing another skill selection on them. No rogue? Anyone with Skill Training can be a trapfinder!
The most fun I had playing 3e was running a character whose "build" would probably make you powergamer types hurl; never mind what would happen in game when her Wisdom 7 showed through, a frequent occurrence! Arguably the best character I've ever had (out of quite a lot, both 1e and 3e), and I wouldn't change a thing about her.
7 wisdom? I'll wager she wasn't a cleric, druid, paladin, monk or ranger then. Unless she was sorcerer, wizard, or bard, her will save was toilet. (-2 at 1st level, +3 at 20th barring a cloak). I guess she got charmed, held, feared, dominated, dazed, sleepy, and otherwise indisposed alot right?
In 4e, as long as your charisma was decent, you could dump stat wisdom and still not go running everytime a dragon flexed its Awesome Prescence around you, or always seem to trust the pretty girl in the dungeon with the sly look in her eye. (Of course, you could if you wanted, but your not being forced to attack your allies because of it...)
I guess I have a hard time understanding why, "for story purposes" you'd ever really want to gimp your character? Isn't D&D deadly enough without playing one arm tied behind your back? Do you really want a PC who can't do his job (heal, tank, nuke, trapfind) on your team? It just always seemed to me that while munchkin super-optimizers are poor examples of play, sub-optimal PCs are just as bad.
You may disagree, but once you lose a PC or two to someone's "character design", you begin to question how viable 10/10 fighter/wizards REALLY are!