The reason Fireball and Magic Missle are popular isn't because they're overpowered. It's because they are effective damage-dealers in a battle. And most characters choose things that help them survive or help them kill over things that help them make ropes do a lil' jig.
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It'd be kinda analagous to saying: "What?! A Greatsword is only a Martial weapon? What the hell? All Fighters who want to deal damage in combat should be using a Greatsword! Quick, increase it's cost so that they're not reliant on it! Make them use weaker stuff instead! Greatswords should be Exotic!"
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The spells are popular because of the niche the arcane caster fills, not because there's something too good about them. Any time you have an option to go with something that hurts things or helps yourself over something that...say....makes pudding...as an adventurer, you want to kill and live, not make frickin' pudding.
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Again, to use a Fighter analogy: "Why doesn't everyone go with Power Attack-Cleave-Great Cleave? Or the Whirlwind Attack chain? Or the Shot feats (if they're ranged). Obviously, because every fighter chooses these feats, they must be too good, and thus they must be bumped up to compensate for their goodness."
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A Fighter who doesn't go with a chain like that isn't maximizing his butt-whoppin' powers. Likewise, a wizard who opts not to cast magic missile is loosing out on a portion of his class's *point*: to cast the spells that make the peoples fall down.
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just because something's popular doesn't mean it's overpowered. Just because fighters like using swords or rogues like hiding or clerics like healing doesn't make swords, the hide skill, or healing overpowered. It just means that it gives the player a power that is, in most campaigns, more useful than others. In most campaigns, zappin' a foe and makin' him keel over is more useful than, say, a divination. If you want the spells to be more rarely chosen, it's a campaign issue -- change the campaign to be intrigue-based, or maze-based, without that many things with hit points to blow up. Be sure to warn your players. You'll probably find more divinations and enchantments because they'll be more useful.
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It just so happens that most campaigns include a healthy dose of butt-kickin', and if an arcane caster can't do that, what's the point of having an arcane caster around at all?