I posted this at such a late hour - and from my iphone lol. Awful misspellings and poor sentence structure that I have yet to correct. Such is life.
As the coffee begins making its way into my bloodstream, I will clarify. I have been using vintage-hot humbuckers for the past 6 or so years. Prior to that, I have been using fairly hot ones such as the DiMarzio TZ/Evo, EMG 81/85, Rio Grande BBQ, JB, etc. I stepped away because I was limited to one guitar and it had to do it all exceedingly well. I began looking for something less hot and more organic.
As it pertains to my studio work, I have found pickups like the Abraxas more than adequate for heavier styles. With a bit of increased input gain from my interface, compression, EQ'ing, etc, the Abraxas can find itself rising to the top in any given musical situation, with the exception of highly technical speed metal/thrash. The low end is a bit loose for this, but sometimes that blurriness is appreciated. Since I had two guitars with identical pickups, albeit two different configs (HSS vs HxS), I decided to dedicate one to the more extreme side of life. Truth be told, I was recently reminded of my love for the older Thrash tones of Exodus and the like. I want to bring back that old aggressive tone, but in a new way.
I've spent the last 3 years refining my recording and production skills and having recently listened to all of my old favorites with new ears - with ears that can sense the backend engineering/production, I am so motivated and fired up to get cracking on some new instrumental metal work. I need a pickup that has that old, raw, tight tone - but with a dash of organic goodness. From a recording perspective, the MM is perfect - if I need more of any particular frequency - if I need to alter the attack or feel, I can do that from my desk. I literally installed it, threw on some 11s and tuned up. After a few tweaks, I was getting some really inspiring tones. If I find myself in need of this tone live, I may have to look for something with a bit more upper mids since I play primarily lead lines. Truthfully, the Abraxas covers all of my bases live, so I think I can stop here - unless someone tells me I need to try the ceramic NB for the studio.
My review of the Trilogy was not even handed and I hope that disclaimer made its way to the bottom of my original post. I played it through a 5150 and modded Marshall with some boost pedals cooking the front end, so no clean audition was done. Where the 63 would sparkle through this rig, the Trilogy was exceedingly dark. It's simply a case of not balancing EQ settings with the new pickups installed, I'm sure, but my expectations of singlecoils are always vintage, so how fair am I? I literally bought this one to balance with the bridge, which it does. I will find some great metal tones from this one once I play around with it in the studio.
Im going to finish tweaking this guitar for this purpose and will inevitably have to bring in another studio queen for lead work. I've been eyeballing some older Ibanez 540s for this purpose! I have no problem with throwing a Crawler into the bridge. That might be one of my favorite lead pickups of all time.
Cheers, brotha.
This pickup doesn't give a damn what you want to play. It showed up to the party to drop a turd in the punch bowl and it's going to hang around to watch who fishes it up on the ladle.

It seems we've experienced very similar pickups and it's interesting to see that your experience of them mirrors mine very closely. I've always felt that the Miracle Man, Holydiver, Crawler and Abraxas are closely related, though I have no direct experience of the Abraxas. All are smooth, the Crawler and Miracle Man are more saturated, the Crawler and Abraxas are richer and more vintage, the Holydiver and Miracle Man are more modern, the Holydiver and Miracle Man are tighter and all of them are relatively thick with the mids playing an important role in their tone.
The Miracle Man is certainly the least versatile and while I can see why there is an association with EMG (other than the name of the pickup), it's so much more organic than an EMG.
My experience of the Trilogy Suite wasn't quite the same as yours as I really liked it, though I confess I prefer the noiseless ones I have in my Strat now. What is it about neck humbuckers you so dislike? It sounds like you might get on with a Holydiver neck pickup as that isn't particularly hot, isn't particularly thick at all and has some lovely highs. Actually, and I'm sure you've realised this already, if you decide you need a step back from the Miracle Man, a Holydiver in the bridge would be an excellent option.