So, first you major create a glass apparatus which has a large vat, a series of tubes, each dangling flasks with a weak connection to the tube (such that you can score and break it off easily). Next you major create say acid in the vat, it flows down into the flasks, you score and break the flasks off. This is seriously nothing a little creativity can't solve (generally the case with major creation).
Okay, so now you needed a craft check to make this huge and VERY complex glass apparatus with tangling flasks and all that. That is masterwork (DC 20) at the least, so the Wizard probably has to blow a Magecraft Spell as well to craft it successfully. And of course the Wizard has to be able to reliably hit the DC to make the various substances.
So at this point he's probably blowing a first level spell and two fifth level spells, and the potions last 1 hour per caster level before their vials suddenly vanish and douse the area in liquid if they're unused. Furthermore, all this only gets you one type of substance, so if you're fighting something fire immune early in the day (and thus use acid) and then find some acid immunes later, you're in trouble.
Surely you can see this is a major resource expenditure just to make your build viable at all. And of course the build is in serious trouble if there isn't a Wizard 9+ or Sorcerer 10+ in the party (which does happen!). I mean, Archivists are really powerful, and would clearly be stronger than Wizards... if they always had a Warlock in the party to give them whatever spells they need. But they don't always have that, so they're not always stronger.
Alchemical fire is the hardest, because of what it is.
Yeah, that's the other thing, this operation sounds more dangerous than a meth lab.
As to the nature of the materials:
Acid - there are lots of acids which are not from animals. This is not a problem. In fact, I can't think of a single acid unique to animals which would deal damage, because acids used by animals are weak. Concentrated HF is probably what we're talking about, which is a really nasty acid, and easily produced by major creation. (Alternately, H2SO4 could work, also produceable by major creation, not as dangerous to work with).
Ah, but Hydroflouric Acid isn't a vegetable or mineral, which are the only things allowable by the spell. Major Creation is great for making Black Lotus Poison (because it's a vegetable) but the only Acids you can use are specifically vegetable or mineral (with the note that by mineral they mean metal, stone, crystal, etc, as stated by the spell). So... no acid for you, here, unless there's some plant creature that secretes acid (there might be, I haven't seen one).
Alchemical Fire is certainly Phosphorus in some form. The degree to which this form is a liquid affects the ease with which you could major create some useable potions thereof on the fly. Of course, that someone is producing them somewhere in the world implies this stuff isn't as impossible to work with as pure phosphorus. Note that phosphorus is also not an animal product.
Okay, so you've got some phosphorous, but what else? Again, you can only use vegetables and minerals. I'm not sure pure elements would count.
I can't speak to alchemical frost/electricity because I don't have a good feel for what they are. I'd have to guess alchemical frost is a substance that evaporates so quickly it chills you, which means its a liquid and thus works easily in the above set up. You will have to stopper said flasks quickly however, probably by melting them shut rather than scoring and breaking off (actually, melting shut is a great idea except in the case of phosporus - flames + phosphorus = bad idea).
Again with the whole "this is like a meth lab set up every day" issue, combined with the fact that you still can't show this is even legal to create with Major Creation. And the massive resource expendature... on a 9th level Wizard, you just took out his top level spells.
I mean, yes, major creation requires us to know something about these substances. But anyone familiar with some basic chemistry can arrive at the only plausible candidates.
I don't think you've done so yet... and remember, Chemistry doesn't exist as a field in D&D. It's alchemy there. Not only that, Chemistry may not exist at all. Remember, Physics doesn't work there as it would here (the sun travels around the planet, usually. Gravity is all kinds of weird, and can be tampered with. Thermodynamics don't really exist, as creating matter is actually very simple. And so on). So why do you assume Chemistry does?
But yeah, if the only reason rogues aren't a higher tier is because they can pull off this kind of operation when supported by Tier 1 clases if the DM reads Major Creation in a liberal way... then I think Rogues are set just right.
JaronK