First of all, don't feel like you aren't contributing good discussion - you absolutely are. This is really important and vital stuff for high-level play. I think that many people thought like you (heck, look at the people who posted in this very thread that said they'd go alchemist).
Alchemist is often seen as a power card with wars fought over it. But it often isn't all that great. Compare it to Laboratory. It's strictly better than lab if you ignore costs (and possession, which hey, we do when talking about which cards are better). So look at the cost. 3p is a bit harder to get than 5. But more than that, you have to waste 1+ turns getting potions (instead of say silver).
But compare it to lab. Lab is, of course, really good. But if all you have is Labs+Big Money, it's actually not all that great. Smithy is better. You need to have a terminal you want to spam. Same thing with Alchemists, except that since you have to go out of your way for alchemist, you need to have something to slow the game down, too. Labs fall into the natural progression of a big money deck better - 3 is silver, 4 is militia until I have 2 (then silver), 5 is Lab, 6 is gold, 8 is province. Alchemists you have to restructure for, and this takes time.
On the trashing point, the reason why trashing should help BM more is that it doesn't speed up the amount of time it takes to get your chain going all that much (still have to waste ~6 turns getting the potions and alchemists, plus one for the trasher, three for some money, an extra turn or two for trashing itself and... after 11-12 turns you can start buying a province every turn). This puts you a turn or two ahead of what BM could do WITHOUT trashing, and with it, BM's still going to have you beat by 2-3 turns. Maybe in colony games the pendulum flips and it starts helping the alchemists more. But province games are just so short.
On the Council Room issue, I've sort of outlined above why you really want an attack for your terminal, but also CR is going to help your opponents an awful lot when you're playing it every turn, and it doesn't help you when they're playing it if you were drawing your whole deck anyway. Moreover, it doesn't speed your deck up more than theirs; it's more like the same amount as theirs, and since they were faster to start with, this magnifies their advantage in a way that should at least compensate for the added smoothness of your deck.
But good questions to ask, for sure.