I don't know that most of these need "fixing." In fact, many of them already have re-designs in newer sets that used a similar mechanic but to greater effect. Cartographer is arguably a better Navigator, Bandit is a better Noble Brigand (that's how bad Thief was. It needed TWO redesigns.)
And more than half the list is terminal money, which really should remain nerfed. If made too powerful, then really boring money strategies would start to outperform more interesting and nuanced engine strategies. I mean, if Mine was $4 and you could reliably open with it, it would speed up BM significantly. Especially if you opened Mine/Silver and could trash four Coppers in your opening shuffle and start copying the Silver (sorry, couldn't resist.)
Just because a card is frequently ignorable doesn't mean it's bad. Who hasn't used Beggar/Gardens or Beggar/Triumph? Mandarin/Capital? Cache/Counterfeit/Banquet/Tower points for emptying the Copper pile in a 4-player game? (Ok, maybe that's a stretch, but it happened.)
Maybe some of the cards could be made slightly more attractive without breaking the game when they appeared. Harvest might honestly be broken if it had +Action. it would almost always be better than Gold and would almost certainly make a BM "Province rush" better than most engines. And Masterpiece gaining any <=3-cost card instead of Silver would be bonkers broken. Pay $7, gain four Encampments? That's a big nope!
The only cards on this list I would be tempted to improve are the ones that would make the game more interesting, not less so. Here are some possibilities:
Royal Seal : $4? Topdeckers are really interesting. Scheme, Traveling Fair, Courtyard, Tracker... these all potentially create very interesting situations for setting up combos. And hey, they're all cheap. I don't think a Royal Seal you could open with would break anything. But it's just too expensive to be worth it when competing with other $5-costs.
Philosopher's stone: Count ALL cards? It's useless in an engine. Single-card economy exploders like Bank and Fortune make engines especially attractive; adding one more treasure to this category couldn't hurt.
Transmute: Add a "may" to the gaining? Breaks the flavor, though.
But honestly, Donald X spent a lot of time and energy designing these cards and playtesting them, and it's likely that many of these ideas or ideas similar to them were tried and rejected.
In fact, second-guessing D.X actually belongs in a whole separate section:
http://forum.dominionstrategy.com/index.php?board=11.0This whole thread should probably be moved to "Variants and Fan Cards"