I guess I can maybe be of some assistance here as I own a Jackson SL3 so although it's the cheaper Japanese cousin, it's still maple neck-thru with alder wings and OFR so it can't be a million miles away in terms of tone and I've tried quite a few pickups in it. The guitars aren't dark but they can be flat so I certainly recognise what you're saying there. I think that maple must be a really difficult wood for a pickup to cut through as everything I've tried sounded better in other guitars. Anyway, here's a rundown of my experiences with pickups in maple neck-thrus:
JB
Flat, dull and could turn to mush under gain. Nothing special at all but sounded a LOT better when I dropped it into a Yamaha Pacifica. It really made that guitar come alive but you're right, it's not for your Jackson.
Alnico Nailbomb
Bright enough to cut through any mix and as tight as hell. VERY aggressive sounding with a real 90s Metal, hairy feel to it. Not particularly versatile in the Jackson but good if you liked that really aggressive, tight sound. Not for me in that guitar so I sent it back.
Holydiver
Awesome pickup. Tonally in the same ballpark as the JB but significantly better in every respect. A thick sounding pickup with plenty mids which some may find too much on a neck-thru Jackson, which is naturally quite middy anyway. Fortunately I like mids. Very articulate but once I got a PRS with a Holydiver I started wanting something with a slightly more aggressive edge to it.
Miracle Man
This is what currently resides in my Jackson and it works beautifully. The slightly scooped nature of the pickup complements the middy nature of the guitar so you end up with a sound that is quite thick, smooth and balanced. It's tighter and more aggressive than the Holydiver but retains that thick smoothness while not having the balls out brutallity of the Nailbomb.
Emerald
This was actually bought for a PRS SE Custom 24 (mahogany body, maple neck) but while the Emerald neck was fine, the bridge version was way too bright. I tried it very quickly in the Jackson and while it cut through that flatness of the Jackson very well, it could be a bit bright and shrill. I'd only use the neck version myself unless it was in a Les Paul style guitar.
Cold Sweat
This was actually in an Ibanez rather than my Jackson but it was still a maple neck-thru with locking trem so I think its inclusion here is warranted. Like the Emerald it's a bright pickup but it's not as open or shrill sounding. Less compressed or thick sounding than the Holydiver or Miracle Man but if you're considering an Emerald I doubt if that bothers you. It was very articulate, cut through the maple beautifully and had enough openness left to give at least a suggestion of a super-hot PAF.
Out of all those, I like the Miracle Man best in my Jackson but if you want something a bit more open and brighter, I'd look to the Cold Sweat instead of the Emerald. If you used a Cold Sweat bridge, an Emerald neck would go really well. It would with a Miracle Man bridge too.
Final two tips:
1) Get your pickups open poled. Getting covered pickups on a maple neck-thru just makes it harder for them to cut through in my experience and you're stuck with that 'flat' sound you want rid of.
2) Install BKP 550k pots and a Jenson BKP 0.022 capacitor regardless of what's in your Jackson stock. It REALLY helps.
