|Mort the Cleverly Named|
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The "philosophical" element is that I've always felt prestige classes should be, well, prestigious.
For many prestige classes, prestige can and should be a part. However, I would argue that for the most part Eldritch Knight and Mystic Theurge just create analogues of old 2e multiclasses, Fighter/Mage and Mage/Cleric. I don't feel that "Eldritch Knight" has a sudden moment of increased prestige when they enter the class, they just continue what they were doing but level their abilities at a different rate. So the question, then, is pretty much just one of mechanics, which people are arguing (and I agree) are better this way.
I'll agree that using an SLA to get in is weird. It is a mechanic a new player will never be aware of on their own. It is narratively weird, since even if one argues the race is "inherently magical" and thus should enter faster being even "more magical" with a higher level SLA might prevent you from doing so. Similarly, as Gregory Connolly said, it encourages forced choices even with no thematic or mechanical link beyond this obscure ruling.
Ideally then, I would hope the FAQ gets changed while the actual requirements on the classes get lowered. This would fix the weirdness while preserving the mechanical change. I know Paizo prefers not to do this to books. However, changing the prerequisites of core prestige classes is not unprecedented, as in the case of removing the "Elf or Half-Elf" prerequisite from the Arcane Archer (as a certain someone advocated). Even if we have to wait until the 7th printing, it is a change that would seem to satisfy all parties.