Not Steel, so I'm not privy to the particular internal debate, but my guess would be that Shifter didn't make it because it's a PrC that only one class
can take. I know there are others, but most PrCs are takeable by a decent range of classes. You can come into Shadowdancer, for example, as a Rogue, Bard, or Monk very easily, and with a Ranger with a few cross-class points in Tumble.
To be incredibly general and vague

, there are two types of PrCs: specialty PrCs (new shtick not specific to one class) and combination PrCs (a PrC that more or less combines two classes). Specialty PrCs (like the Shadowdancer, for example) need to be accessible from several different core classes or class combinations in order to have enough "A lot of players will play this class" potential to be worth the scripting time. Combination classes (like the Eldritch Knight or the Arcane Trickster) can be pretty class-limited (with Arcane Trickster, you need Sneak Attack, so it's Rogue or nothing) as long as the class they're limited to is a popular one.
Shadowdancer: Bard, Monk, Ranger with a few Cross-Class points.
Eldritch Knight: Bard, Wiz/Sorc, or Wiz/Sorc+(Fighter, Paladin, Ranger, Barbarian)
The Shifter makes great sense in a pen & paper game -- all the work is on the player's part. In a CRPG, though, the Shifter is an expensive class (programming-wise) with some fairly unique abilities (all the polymorphing), and the only people who ever see it are druids who want to do something beyond straight-class druid. That's a narrow enough niche that I can understand it not being worth it from a design perspective.
Probably more than you wanted to know, but that's how these decisions get made, generally. The Eldritch Knight may or may not have been a pain to code, but the programmers knew that a lot of people might see it, because a lot of wizards and sorcerers (and a few bards, too) would be willing to lose a few caster levels to be a decent combat-badass as well, and they could do so by adding fighter, paladin, ranger, or barbarian as well. That's a lot of potential class combinations that make Eldritch Knight viable.