I would like to somehow have the option to include them in full random. I agree that they should not be part of the free base game package, or the Intrigue package. I don't know the new payment model. Are all expansions going to have a one-time cost? Maybe give some cost to these 12 cards to, like a mini-expansion.
The reason for removing these 12 cards was surely to make the two first sets better, especially for new players. (One aspect of this is that in the base game, 5 terminals and 1 non-terminal were replaced by 3 terminals and 4 non-terminals.) The reason for removing them was surely not to make playing random with all sets better. At best that had to have been an afterthought.
I would categorise them in four tiers:
D) The only cards that are almost useless and can be beneficially retired are Thief (is "fixed" in Noble Brigand and now Bandit too), Adventurer and Scout. (I have never once bought an Adventurer. Even when I was learning Dominion and knew almost nothing, I saw that Gold is always better.)
C) Cards that are almost as useless, but I don't think it hurts to keep them, are Chancellor , Spy and Secret Chamber. They have their uses a bit more often, but they could be retired too. At least Storeroom does Secret Chamber's trick.
B) Cards that perform a function that it would be a bit sad to lose, although they rarely matter, are Coppersmith and Saboteur. The thing is that no other card does what they do (including the new cards), and figuring out when to go for them is a cool possibiltiy to keep. As long as they are not in the first two sets that players buy, I don't see the problem.
A) The cards I'd hate to see go are Feast, Woodcutter, Great Hall and Tribute. Feast and Tribute are useful quite often, and also each do something no other cards do, especially Feast. Woodcutter being the only source of +buy has real impact on the game, since it's cheap but weak and terminal. That happens quite often. Great Hall has an impact on many games. Often you want cheap cantrips, and even more so if it gives VP, and quite often the types matter too. The sole fact that they don't clog your deck means that they are a pile that often gets emptied and that changes the game too. (Interestingly, Mill is priced as if using Great Hall as a baseline.) Ok, Tribute and Feast Great Hall have "fixed" versions, although Courtier can never be a Village (big difference), and Mill costs more (smaller difference but not insignificant). In the end Feast is the #1 card to keep for me.
EDIT: fixed wrong card name