I would tell you to keep both, but, hey, I'm biased - Chemistry and Ancient are my favourite (and strongest) subjects. xD
To be honest, if you absolutely HAD to choose, I'd pick Chemistry over Ancient History.
1) Humanities are usually riskier than the sciences unless you're topping/near the top of your school for that subject. Why? For the sciences (especially for Chem), the syllabus is THE Bible, and, therefore, as the questions will not diverge much from it, Chemistry can be more predictable. Which is good, if you're a straightforward, hardworking fellow.
With the humanities (although this doesn't apply as much to Ancient, as it has more memorising than Mod. does), due to an arguably more "wishy-washy" syllabus, they can be harder to predict; it's more likely than in Chem that the exam would send you a left field question. I know that this is a controversial statement, but that's what I've seen in a lot of cases.
2.) Scaling. A petty reason, but if you're serious about Med, it is something to take into consideration.
Such a pity you have to choose between such awesome subjects though. Why can't BOS just let us drop English Adv/Standard instead? The AOS is killing me (although Modules are okay so far). D:
P.S. If you're 12+ units, don't do both. Unless you're extremely time efficient, outstandingly intelligent, or uber dilligent, 13-14 units (particularly with a Maths and/or English ext. unit) will start to take a toll on you. That's why I'm dropping 4unit English. :/