I would say allowing both 5/2 and 3/4 starts is the more questionable design decision. There's just little necessity for it.
Indeed, all of this discussion about Chapel's cost, Ambassador's cost, and the like, boils down to one question. The First Question--the oldest question in Dominion, hidden in plain sight. Why is the opening split allowed to be different for different players?
This is so obviously a poor design decision from the standpoint of a competitive player, but
Dominion was not designed with the competitive player in mind. The reasons for this oversight do not arise from competitive play, but from more basic design rules:
(1) Without Estates in the starting deck, there are no real choices in the early game. OK, you have $5 and... $5. Trashing becomes less important. Card costs have to be revised upward significantly, and even so you're probably buying two copies of the most powerful card available at $5. Oh, and you're pretty much guaranteed $5 or better for every later turn, so really, cards costing less than $5 become silly.
(2) With only one Estate in the starting deck, you always open $5/$4. This isn't quite the same problem as above, but it comes close; costs of cards still have to be a bit higher, $4 is the lowest price point, and trashing is still weak.
(3) With two or more Estates, you have the possibility of uneven splits.
ISTR Donald saying that the general consensus in early playtesting was that 4 Estates was too little cash to start with, while 2 Estates led to some of the same problems in (1) and (2). Now, the rules could still force an even split (3/4 for everyone or whatever) but this is a mechanical problem. Dominion is a very, very simple game, and adding a starting rule that forces a particular split makes you play two turns of Kinda-Dominion-But-I-Don't-Have-to-Really-Play-the-Cards before you get into the real turns. While this is technically simpler for the players to carry out, it requires a special rule, which makes it mechanically much more difficult, especially for those just learning the game. And since players who just want a fun game don't really care about these tiny balance issues, and those are the target market, unbalanced splits were left in rather than adding in special start-of-game rules.
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Ideally, competitive Dominion uses equal splits for all players. In this game, the costs of Chapel, Ambassador, Masquerade, and other extremely powerful openers
does not matter in terms of balance. If there were always equal splits, you'd take Chapel at $2, $3, $4, or $5 if you felt it was viable, because your opponent has the same opportunities.
Which is why competitive, ranked Dominion should have equal splits: a 1/6 chance each of 2/5 or 5/2, and a 1/3 chance each of 3/4 or 4/3.