Depending on the rest of the game's design philosophy and what you're attempting to bring to players. One perspective you could explore is interdependence. You could explore use based skills easy to track these with multi-point scale graphing (could be in game or for dev use) player will focus on areas of expertise allowing them to accomplish certain tasks with great ease, while other tasks or objectives with multiple tasks will require a team or shift in game play focus to complete. This still uses a level system but since its 'use based' the impermanence of unused skills scales them back creating a dependence on other players who've focused in that area. Using in fiction visual feedback to express not only skill focus but skill level could do away with the usual number based depiction of excellence. I was mostly referring to a role playing or action game but this can also carry over to RTS or more tactical games. Making certain types of strategic combat (guerrilla, spam, tech up, etc) a skill focus and making a focus on one type of strategy open up abilities that apply to that style of strategy. Like a use based tech tree.
I think some amount of lvl progression has to exist as I see this as a part of every game's exploration. Even if it's just unlocking different combinations of controls.