I've had the same problem with the JB...cool for mahogany but sucks major balls with alder.
among others I have 3 alder-bodied axes (Jackson SL-1, ESP MI custom and a customshop ESP MII DLX) I'm playing EMG81 in those and am pretty satisfied with that. with mahogany you won't get the "bite" you've got with alder---neither is better, it's just a matter of taste if you like that low punch more go with mahogany, if you prefer biting growl go with alder.
Mahogany gives more "wall of sound" and alder cuts thru better in the mix.
I personally learned to love swamp-ash guitars (the good ones), they have little mids extrem punch (similar to mahogany) but way more clarity and definition...somehow like best of both worlds.
I wouldn't say alder sucks for metal...of course it's easier to get a creamy liquid tone with mahogany but alder also has some qualities that aren't bad.most signaturegutars are made of alder or mahogany I'd say the majority of Jacksons and ESPs (at least the superstrats and rhoads models etc) are made of alder and that are the typical metal guitars, so alder cant be that bad huh?
just have a look at the signaturemodels and see what pups they use
this might be a good read:
http://ultimate-guitar.com/columns/the_guide_to/ultimate_guitar_guide_tone_woods.html
so is this:
http://www.jemsite.com/jem/wood.htm
you could try that one, too.
the pup recommendation together with their tonechart should give you a ruff overview what to look for with a pup