For Cornucopia & Guilds 2E, was there ever any concern that either of the two halves would have more content than the other? Cornucopia having 5 removed cards to Guilds' 3, for example.
No; the idea is to not ever split them back up. So e.g., one Reward uses Coffers, and that's fine.
Hindsight being what it is, had they initially been big sets, what would you have wanted to do differently? And if you never had small sets, what would a larger Alchemy have looked like?
It's hard to say what they might have looked like; they'd need more stuff going on, and who knows what that is. Cornucopia's "variety" is invisible, so the other theme would want to be very visible; Guilds' coffers and overpay are both very visible, but a large set probably would still have had a little something more going on.
Alchemy was large back when. At the time that meant 20 cards; there were a couple versions at that size. A key thing is, it didn't actually have more potion-costing cards. It had a few potion-involving cards, and some other cards that kind of hung together, including Festival / Library. However, at the point where they wanted small expansions and Alchemy became one, the set had lost some cards to other sets, and so if it had stayed on schedule as the expansion after Dark Ages, well I don't know how it would have shaped up.