Debating between these 2, I like Schecter so that's what I'm thinking about. Which one do you think has the best pickups, and which one do you think is the better one overall?
Thanks in advance!
The Damien Elite is way better.

Way better pickups (EMGs instead of Duncan Designed actives),
Graphtech nut and Tonepros bridge (this stuff makes a big difference).

You get a hell of a lot more guitar for only $100 more.
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(For fans of Death/Groove/Prog Metal)

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Are active pickups good, specifically the one in the Damien Elite? Because I honestly have no idea.
^ They are good if you like them. It has to do with the sounds you are after. The downside of actives is that they require batteries. If you play extreme metal, actives may fit you well. To get a good idea if you like them or not, go and try some guitars.
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^^They take just a standard 9v battery. $3-4.

It's a total non-issue. The battery in my Schecter has lasted since I bought it over 1 1/2 years ago. I play nearly every day too. I always pull my guitar cable out of the guitar when not playing though -- that will drain the battery faster. Effects pedals drain their batteries MUCH faster than active pickups.

As for sound, they are great for certain things. The EMGs that the Damien Elite comes with are pretty much THE standard for modern metal. They are very clear and tight sounding for some very precise riffing. They don't influence your EQ balance that much. Since they have an onboard preamp, they will push the first gain stage on a tube amp (or any amp, for that matter) harder than most high-output passive pickups. This can result in more distortion even with the gain turned down on the amp.

Some people find that they can sound a little 'sterile' on clean settings. I agree, they can. But some tweaking of your EQ, guitar volume knob, and some effects like reverb, delay, and chorus will warm things right back up.