Actually, there is no exact answer to your question, only suggestions and things you could take into consideration. I have only got three guitars but way more pickups, so I change them very often, therefore I'll be saying some things about pickups and usual misconceptions. Note that all I say reflects
my personal oppinion and should not be seen as a universal truth.
Important thing about pickups: Every pickup combination will sound different in each guitar. The tone is also dependant on what amp, string gauge, picks etc. you're using. Whether you like it or not is a matter of taste - and genre.
You need high output pickups in order to get a "brutal metal tone".
Wrong. Medium output pickups or even so called "vintage pickups" (kind of low output) can give you a very sweat tone. I don't know what you mean with "crushing metal tone", but not too high output pickups can help you get a very tight (not muddy) tone. You could hear every aspects of the guitar itself and the chord you're playing, while high output pickups could undermine the qualities of your axe. However, high gain and high output hide sloppy technique or can be a lot of fun - as I said, it's also a matter of taste and genre.
Active pickups (e.g. EMG) generally higher output than passives.
Wrong. Let's take the archetype of active pickups, the EMG 81, as an example. Its headroom is very limited, in other words, it compresses a lot, which will give you the feeling of being high output, but what it really does is give you about the same amount of output, no matter if you pick hardly or softly (example is exagerated). Some high output passive pickups, e.g. DiMarzio DActivator Bridge, have a lot of headroom. You will get tons of output if you smash your strings and you will get considerably less if you caress them. But as I already told above, passive pickups can have compressed headroom, too. And they do sound pretty sweet.
Sidenote: The 18V-mod for active pickups increases the headroom. Also, the new X-series of EMG might react differently to hard picking. I haven't tried either of them, though.
Why would one need active pickups, then?
Active pickups have considerably less noise. But IMO, that is not an argument against passive pickups, as there are a lot of methods on how you can avoid unwanted noise. Eventually, you should use the pickups you like, no matter active or passive.
I've listened to some pickup comparison samples on XY, and I didn't hear much of a difference. Am I just deaf?
No, you aren't. The higher the gain, the less the pickups (and guitar) can be distinguished from each other. However, you will most certainly hear differences when listening to the DI-files. Also, they could feel more different if you were actually playing instead of listening.
Mahagony, alder, basswood, maple, ebony, rosewood ... WTF?!
Before buying a guitar, play it extensively. Also try it out without amp. IMO, wood does make a lot of difference, but what matters in the end is whether you like the tone of the guitar or not.
There are way more things I could tell about wood, pickups and whatever. But eventually, I'll always be saying: There is no such thing as "the best combination for an XY-tone". All gets back to how you as a guitarist handle your guitar and the rest of your gear.
