The problem is a legacy issue. In 3.0, everything not from the Material Plane was an outsider or elemental unless it was a native outsider. In 3.5, the extraplanar subtype was added to open the possibility for extraplanar creatures of other types. Unfortunately, it wasn't used as extensively as it could have due to legacy compatibility. Pathfinder retained it. In Planescape, on the other hand, it was quite common for humanoids and animals and so on to naturally inhabit the outer planes (though the type system in 3E didn't exist then: the only "types" in 2e were animals, persons, monsters, plants, constructs, undead and extraplanar, which could and did overlap); in the 3e Manual of the Planes this lead to oddities like Bauriars no longer needing to eat or sleep and unable to be raised despite the opposite being true in 2e.
There isn't a compelling reason for every creature native to the inner or outer planes to be outsiders. I can understand using the outsider type for immortal beings like genies and demons, but not to the loads and loads of other creatures it is applied to. A dozen different animalistic outsiders in the bestiaries have identical paragraphs repeating that they have no need to eat but enjoy hunting prey as their main form of recreation. Outsiders are defined by lacking body-soul duality: they are physically embodied souls. Fiends are literally made of evil, and elementals are literally made of their element. That doesn't need to be true for every creature from the outer planes any more than it is for fiendish and celestial animals.
Because of the legacy issues, the native subtype has lead to certain problems. The kami subtype from the bestiaries is a native outsider, but unlike other native outsiders they do not need to eat, drink or breathe; it doesn't really make much sense for them to have body-soul duality either. Tritons and Planetouched, as native outsiders, are immune to charm person and dominate person even though they were vulnerable in 2e. The Aoandon, an extraplanar outsider, is explicitly the restless soul of an angry dead woman and would be more appropriate as an incorporeal undead. The Manitou, a native outsider like the kami, is explicitly a nature spirit and thus more appropriate as a fey. The Wendigo is also a native outsider and nature spirit like the kami and manitou, and problematic for the same reasons. (Aside, the 3.5 book Relics & Rituals Excalibur introduces two new types: spirit and manifestation, respectively incorporeal elemental/fey-like nature spirits and physically manifested emotional resonance; the Book of Hell introduces the biomechanoid type, which is just copy-pasted construct type except with the need for fuel).
I think a lot of the confusion could have been avoided if the outsider type was replaced with "immortal," "eternal," "spirit," or similarly less confusing terminology. As embodied souls, immortals draw their sustenance from the life-force in the air and have no maximum lifespan. The native subtype would be unnecessary in this instance.
There is also the larger problem of creature types being bolted to HD/BAB/skill packages leading to problems like certain creature being shoehorned into inappropriate types just because of the package (e.g. half-human/half-animal creatures being various aberrations, magical beasts, monstrous humanoids, humanoids, etc) and fey and undead being crappy at combat. PCs are usually humanoids but don't all use the same HD type, so creature types shouldn't be treated like classes either. Monsters need to have a set of roles that define their HD and skills, so that monsters can be more customizable without being shoehorned into specific types due to game mechanics.
