Milling as a central theme isn't the problem. What you need are distinct variations upon the idea.
For an example subtheme, we can look at "Grind". While it isn't officially keyworded, the term is generally used to refer to a type of milling that cares about the number of lands milled (so you may want to change the name if you want to use what you're using). With this mechanic in place, certain lands can have abilities that activate when they are milled. A set of dual taplands, usually unexciting, can have an ability that allows them to enter the battlefield when they're milled. This adds another level of strategy to using the grind ability correctly.
You may also want to consider the colour identities as well, and how they all relate to milling. White, red, and green will have to be given new mill-centric roles that happen to fit the colours flavourfully.
Blue: indiscriminate milling. Primary goal is to mill mass quantities of cards from opponents, or perhaps to mill oneself to cast flashback spells and such, as a secondary goal. The iconic milling colour. It would be practical, albeit boring, to attach a set number of cards to mill on the usual blue cards that are present in every set, much like how scry was used in Theros.
Black: targeted milling. Primary goal is to seek and remove specific threats from opponents, or to use those threats to your own advantage. Again, with a possible secondary goal of searching and discarding one's own cards to flashback, reanimate, etc. Targeted milling cards can take the place of the cards that discard, which are present elsewhere, as a prominent subset of black cards. Reanimation also becomes a lot more relevant.
Red: whereas black is known for being suicidal with life costs, red can do this with milling themselves. Alternate casting costs, and abilities that trigger upon being milled are something to consider. Possible balancing required in the form of negative static abilities being applied by cards while they're in the graveyard. Fast-hitting, but stalls out when the game progresses too long, as per the regular red.
Green: recursion from grave can be a primary goal, where the cards are first milled and then put into the hand. In this manner, green can possibly be better at "drawing" than blue, given the right setup. Secondary goal can be to have permanents that care about the number of cards being milled, e.g., Tarmogoyf-like creatures. The focus is less on depriving the opponent or setting a timer against them, and more on pooling one's own resources.
White: probably a focus on exiling cards from the library, and exiling cards in the graveyard. An interesting idea would be for white to mill exactly as much as needed, such as by having you declare a quality, and if something among the top X cards of the library have that quality, it's milled or exiled. White removal can be focused on delaying, on the surface, by sending cards back to the top of the library, only to have them be milled by another ability. Good candidate for the combo-centric colour.
A story about the setting would also be nice. Why is the plane mostly populated by creatures that have the ability to perform psionic lobotomy?