|Archmages don't bother with puny magic missiles.|
See, in the beforetimes, a wizard could memorize a number of magic missile spells, a number of fireballs, and so forth. Even with Spells and Magic, a wizard had a sort of finite spell memory.
The idea of Heightened Spell is using spell slots of higher level to cast more potent lower level spells. But what's missing is the theory for why a wizard can memorize Magic Missile as a third level spell for greater effect.
Maybe the idea of finite memory isn't the best of theories, but it seems to work. I mean, we're talking about magic, after all. Even when memorization became spell preparation in third edition, it still doesn't quite make sense why you might allocate more of your fixed spell preparation/memorization power to a more potent Charm Person.
This is one issue of the idea of quadratic wizards: as they gain levels, not only do they gain the ability to cast higher level spells (Magic Missile to Fireball), but they gain more spells (3 Magic Missiles and 2 Fireballs) and the power of their basic spells increases as well (Magic Missile now creates 3 missiles instead of one).
So Heightened Spell fixes some of this. Magic missile can be memorized with a first level slot as usual, or a third level slot for heightened effect. The issue here is tying the mechanics to the story: why is this possible?
Furthermore, why aren't wizards getting more powerful as they gain knowledge? Either there's one magic missile spell and that's it, there's multiple magic missile spells (MM1, MM2, MM3, etc.), or as a wizard gains more arcane knowledge, his spells grow more powerful. Now, this is going to change with your theory of magic and the story, but the Heightened Spell option seems to indicate that its the multiple spells option in Generic D&D, though that's a bit of a surreptious interpretation.
In terms of a rule-based solution, my preference is for simplicity and elegance. That means for the quadratic wizard problem, a simpler solution is better. This would be fewer spell slots and letting them automatically scale with level. Ditching leveled spell slots is certainly simpler, and D&D has quite the history of spells increasing in efficacy as the caster increases in power. Furthermore, reducing the number of spell slots will also keep things simpler for the most powerful magics a wizard uses.
|Even Pathfinder wizards carry crossbows.|
So a wizard might be able to cast one spell per level (in addition to encounter-based cantrips), but the magic missile spell might be as viable as fireball. So the wizard still may rely on a scimitar, staff, or crossbow at some point when his limited selection of powerful spells are exhausted. Sometimes a weapon is just better, and wizards may even have many an enchanted weapon. This idea might be a little too Appendix N for modern tastes though.
In this system, spell memorization might be recast as practice. Wizards can keep a certain number of spells in their brain, but without regular practice they tend to forget them. Wizards would still retain the benefits of a versatile spell selection each day, and the system is a bit simpler since they're tracking fewer slots and use their caster level for all the calculations. This can still be combined with versatile and situation cantrips, and ritual magic for a complete versatile wizard package.
Sorcerers, too, might benefit from this system. They have a smaller number of spells known, but still cast them all at their maximum caster level. Rather than simply extra slots, Sorcerers could be given an alternative benefit, such as one free spell each encounter. A sorcerer, then, would always be able to cast one spell each encounter, though still with the limited selection.