A few things, then.
The Earth/Stone issue is one that rankles. Yes, it can be explained away, but if it were better addressed in the first place there would be no call for half-baked in-game explanations. This is also true for the "Chaos elementals? Are they necromantic?" issue that pops up. I mean, by the rules they are. It's unavoidable. Chaos as a damage type is in the Necromancy effect group. Boom, end of discussion. But Chaos as an elemental is opposed by Order, an Earth associated element that nevertheless deals heavily in celestial effects, the members of which typically throwing and swinging Prison. Personally, I would like to see at least terminology changes so that there are no longer issues of "No, not Earth as in Stone, Earth as in Healing" hiccoughs.
Personally, I benefit from a better (or at least more definable) visual cosmology. I'd also like there to be "actual" answers to some of the questions that come up, because there isn't much in the game that I personally find more frustrating than being asked "Well, how does this work?" as an in game question, giving what is in our chapter the official answer, and having Traveling Pat from somewhere else chime in with "I heard different." I believe it pulls people out of game to come face to face with "How it works" being up to the imagination (or lack thereof) of plot writers both present and past. This isn't to say that every character in-game needs to know or care, just that I know that I personally and others whom I've spoken to get pretty frustrated by how free form this is. We may represent a minority, but it's still something I'd like to see at least talked about. It's not like addressing this has any impact on game balance in any way, unless someone finds something more reasonable for the Earth aligned Order elementals to swing than a Celestial spell.
In my opinion, the two greatest offenders are "Earth" (healing) and "Chaos" (necromancy). I would propose, if I were to do so, that they be replaced so that the associated incants became "With my spirit's force I <healing spell>" and "With unnatural force I <necromancy spell>". Healing comes from life, "unnatural" doesn't mean "bad" so that conversation remains ongoing, there is no "Earth/Stone" miscommunication, Order and Chaos are now just parts of the cosmology and neither is inherently evil, meaning that neither also seems inherently good by comparison. It even maintains the same syllables for those who truly care. In addition, I really feel like getting away from calling upon the Earth and instead tapping into your very real, very present in-game spirit makes healing less an act that is kind of close to religious prayer and more about "life gives life", which is far more appealing conceptually to me personally.
Please bear in mind that I'm not pushing for these changes. There are too many people who've been playing for too long and are to used to how things are now to try and push through a change like this for essentially a cosmetic issue is unrealistic. There are better uses of the owners' time. I just have my preferences and hot buttons, like everyone else.
By thy way, I don't know about everyone's monster manual, but all the ones I've seen have cards for Air (and water) Elementals.