I do not understand this obsession with 3P. Alchemist and Familiar are strong enough that they are rarely skippable even at 3P. Sure, it is possible for multiple players to go Potion/Silver and one to get an edge by the other missing 3P on the next shuffle. It is also possible to miss 5 when both players open Silver/Silver. Do you complain that Laboratory and Witch cost 5? Indeed, that is even more of an "unfair" price as you can open 5/2 and possibly can a TWO shuffle edge with Witch over Silver\Silver. The generally accepted rule of thumb is that potion converts to 2-2.5 coins. At 4-4.5, Alchemist and Familiar would be even more unskippable than they already are. I'd rather the game not force all (good) players down the same path.
man, it's different. there are reasons why these cards cost 5$. you need to build a deck that hits 5$ early/a lot in order to buy them, and they need to cost 5$ so you can't open with them. And balance is not for powerlevel anyway, it's for fun level.
let's say Alchemist, Familiar, and Stone cost 2$P now. Does this make them considerably stronger? No. It makes them a little bit stronger, but not much, usually when Familiar is good, you just take the risk anyway. Does it change the way you build your deck in any way? Hell no. You just open potion/x anyway. and later, you usually expect to draw potion with 3$ regardless. Does it cause less frustration, because you almost always draw 2$ with your potion, but often not 3$? Yes. So, what's to talk about here?
And if you want to look at powerlevel, Scrying Pool and Apothecary cost 2P$. How does that make sense. If anything, scrying pool should cost 3P$ and Alchemist/Stone 2P$. You see, there is no excuse for the stupid extra coin on these cards.
I don't think it is that much different at all. If you get 5/2 on a Witch (or Montebank or Cultist)/Chapel board and the opponent doesn't that is a bigger edge than getting Familiar a shuffle faster. All 3 of those cards not only junk, but help you get back to 5 for more power cards. People complain about Cultist (because of the stacking not the price), but the other two are not complained about at all even though making them $4 would even the chances of getting them. (I tend to think Chapel should be a 3 cost card to prevent those massive edges, but OTOH if the board has no power 5s then 5/2 would utterly such with a 3 cost Chapel on the board. Chapel is very difficult to price fairly, which is probably how it landed at 2.)
Familiar is considered one of the two most powerful Potion cost cards as is. It is virtually unskippable. I don't think making it more powerful (i.e. reducing the cost) will make it more balanced. And yes, balancing power is a key component to balancing fun. Over and under powered cards aren't much fun - most of the bottom of your list is precisely such cards - because they reduce decision making. In other words, there IS a reason Familiar costs 3P. Increasing the chances of both players getting one on the same shuffle is not worth (further) reducing the decision making on openings when Familiar is on the board.
Alchemist is a strictly better Laboratory. As such, 3P is the most logical choice. Additionally, it is not as crucial to get the first one as Familiar (and all junkers).
Philosopher's Stone's usages are more limited. When its good, it probably doesn't matter much if it costs 2P or 3P (you probably aren't buying it on the first reshuffle). When it's not, you're skipping it either way.
Apothecary is so subtlety strong that years after its release people are only now starting to form a consensus that it is strong. Scrying Pool is fantastic often, but also crappy without trashing. In other words, it is hard to price. I'm not sure changing the price of either changes much.