The fact that full spellcasters (clerics, druids, sorcerers, wizards, etc.) are already more powerful than everyone else means that, really, a few levels worth of spellcasting progression sacrificed for an interesting prestige class is STILL leaving them at a similar or greater level of power than the rest of the party. By the time a full caster can enter a prestige class, he or she is already flinging around 3rd-level spells or better, so they're already contributing heftily to the party with Lightning Bolts, Hastes, Blinks, Flies, Dispel Magics, Magic Circles Against Evil, Protections From Elements, Displacements, Invisibility Spheres, Hold Persons, Suggestions, and whatnot. Not to mention the trusty Magic Missile, Ray of Enfeeblement, Rope Trick, Bull's Strength, Web, and Knock, for instance.
Really, what fighter can do anything similar in power to a wizard casting Horrid Wilting or Summon Monster IX? Isn't the wizard/elemental savant just as well off as the fighter when he's just casting Maximized Fireballs and Empowered Walls Of Fire with similar save DCs and such to those 8th and 9th-level spells? And he's got nifty abilities like being able to stride through the Elemental Plane of Fire unburnt. Sure, he's probably not quite as effective as the full wizard, but he's still plenty effective enough to be useful in the party and not disappointing or burdensome.
I've never had a problem with PrCs that give only partial spellcasting progression. Neither have the groups that I've gamed with the longest (I've gamed with many groups briefly, but only a few for any significant length, and thus only a few long enough for prestige classes to come into play). I'd love to play a Fatespinner, Elemental Savant, Spellsword, or Pale Master (one of my PCs is on his way towards Spellsword, but that campaign went on hiatus some months ago).