My issue with modifying/removing dwarves and elves is that the PC’s may want to play them.
In my campeign setting there is no real wonder of the elves/dwarves because they’re so intermixed with humans that they’re a common enough thing to see. I think that should be the case in any game unless your world has a lot of segragation.
If you want the PC’s to have a tolkenesque respect for elves, bring in grey elves, and let some elven NPC tell the party how amazing the grey elves are. You can do the same with dwarves.
If you want mystery, that race should be something new, and hasn’t been on the plane for long. Add a new species of your own creation, or something obscure from the Monster Manual. Then come up with why they’ve just recently arrived on the prime material. Anything that has been arround for centries isn’t going to have too many secrets.
I use a mostly standard game setting because of the huge ammount of infromation that would be “common knowledge” amunkst the people of the world that would have to be distributed to the players who are allready framiliar with the way the world works in most games.
If you start deviating too far from the standard setting, you’ll have players who are peeved at their inability to predict what is going on. A wizard should know, for instance, that the plane of fire is uninhabitable unless you have special protection. If in your world, it is habitable then you need to explicitly tell him that before he constructs any plans arround it