Can you elaborate how the Workshop with "+1VP per empty Supply pile" ended up dominating games? It sounds totally innocuous to me, so a story or two about those games would be really enlightening!
Some players buy some, maybe eager to get copies of some cantrip everyone likes, like Caravan. The Caravans run out. Now the workshop is making +1 VP. That's attractive so people start getting more of the workshops. The people who already have them want a 2nd pile to run out and help empty the workshops. Now they make +2 VP per hit and there are ten of them in decks so players scramble for points while the workshops empty the Estates.
I had a couple early games that were stupid because of this card. Then for a while the card seemed fine. But we started to see the bad cases more and it was clear that one reason we hadn't been seeing them was because we hadn't realized how good the card was.
I'm also interested in why the version that could gain itself was an issue that needed solving, since there are other cards that can run themselves out pretty easily (e.g. Magpie, Stonemason).
It's not "it's awful that this pile runs out," it's "it's awful that you can choose to run out this pile incidentally." What you want is Caravans. But instead of gaining a Caravan, you trash the workshop and gain a Caravan and another workshop. You're running out the workshops as this random extra thing you're allowed to do on top of what you actually wanted, which was gaining Caravans.
Some players will just automatically do this; they can do it and that's enough for them. They exercise their power. And it sucks. It's anti-fun, so the card doesn't do that.
No guarantees that Gathering cards will ever appear outside of Empires, but should they remain strictly tied to VP? Gathering with coin tokens seems like an obvious thing that could work.
For me Gathering cards want to be things that Defiled Shrine is specifically dodging putting tokens on. So, cards that put VP tokens on their pile. "Gathering with coin tokens" runs into the problem of interacting with Trade Route, but that aside, would get a different type if it happened.
Same question for Landmarks.
Landmarks are intentionally tied to VP.
You could just make cards that modify the rules. I considered it way back when; it's a thing I've done in many games. I didn't do it because Dominion has kingdom cards filling that rule; they change the rules plenty. Dominion doesn't need other rules-changing cards. I considered it again later and still didn't want them.
But I do have Events and now Landmarks. Events can change the rules, but only via the Event-buying mechanism, which is like buying a card without the card; it felt like a reasonable extension. Landmarks can change the rules, but only in these VP-making ways. While they are each a step towards just having randomizer cards that change the rules, they still both try hard to stay within limits, to only affect the game in a way best done via these mechanisms. In general the best way to change the rules in Dominion is still to have kingdom cards that do different things.