Against the Storm by Eremite Games (Steam page, official site) is a popular 2.5D town-building run-based RTS with a Warcraft 3 inspired aesthetic and a deckbuilding meta-game progression.
You spend an hour building a base while fulfilling randomized mini-goals for victory points. When you have enough victory points, you leave that base behind, and restart on a new map to build a new base to unlock more buildings and resource types and perks to add to your shuffled deck of possible choices. This all ties into an overarching "world map" meta to unlock more bonuses.
It's well-made and I can see why it's popular, but design-wise, I feel it's overburdened with too much stuff...