From the ones I have tried, I think the best thing about them is how dynamic they are, and for want of a less generic term, the 'feel' when playing them as they react similarly to a real amp. I agree that they are dark. I have messed with the amp settings as suggested, but only adding treble/presence or cutting bass and mids via the eq can really change this. I attribute the inherent dark character mainly to three things. Anyone feel free to correct me.
Firstly, M Britt seems to dig mostly single coil type guitars, whilst also using special p90s which he says are brighter than standard ones(check the gear videos on his website). If he uses these to dial in his tones then naturally if one uses humbuckers then they will sound darker.
Secondly, as previously mentioned the profiles are catered towards live use, and as such probably sound best played loud. As I'm sure many of you know, our ears perceive relative frequency levels differently at various volumes(google fletcher-Munson curves), and so it's a by-product of compensating for the perception of increased treble during the profiling process:
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At low listening volumes – mid range frequencies sound more prominent, while the low and high frequency ranges seem to fall into the background.
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At high listening volumes – the lows and highs sound more prominent, while the mid range seems comparatively softer.
So it may be that he is profiling them with this in mind, although that doesn't explain the amount of bass that people talk about.....it would be interesting to find out more about his profiling process and how loud he listens back to the tones when engineering and refining in the studio.
Thirdly, as also mentioned, he mostly profiles through his 3rd power cab(are all his profiles done using this cab?). I don't know much about the cab, but given it's a 2x12, and if it is naturally brighter than most, then it would make sense that he may be compensating for this during the profiling process by reducing the treble and/or adding using appropriate mic placement.
And last but not least, he just digs the beefy tones
Personally I think the profiles have been optimised for rock, blues and country and pop type stuff and for tele, strat type guitars they are amazing. However if you're looking for profiles optimised for metal/shred with humbuckers, then it would make sense to look elsewhere. I get the impression thats not really the style of music he gravitates towards anyway.
Edit: It's possible that M Britt may chime in and dispel all of my possible theories, but at least you can tell I've given it some thought haha.