Yes, I expected to have to tweak the Helix - that was one of the sentiments I read about it vs. Fractal in the user reviews before purchasing. Not sure how that's possible.
I have no problem tweaking and playing (and learning) with the Helix. I'm a tinkerer, and tinkering with it is half the reason I bought it.
Just a data point - I put the Seymore Duncan humbuckers in last night, SH2 / Jazz on neck and SH4 JB on bridge, and, well, it was NOT a night and day difference. I guess this batch of Agile guitars did not have such crappy PUPs after all. There was a bit more, I dunno, "clarity" and character - but still very, I guess what they call "warm" vs. "bright". I would almost say muddy still. I know LP guitars and humbuckers are supposed to be more warm by nature but jeez, quite the difference from the Strat of my youth.
I did not change out the pots and toggle switch yet - however I am doubtful those are doing anything too bad to the tone since I have it set at no treble cut. I do plan to do that, however, and will likely put in a new toggle or push/pull pots to access the single coils in them (they are 4-conductor) for more options. Hoping for something brighter. I know a lot of people would say just get a Strat but I've had a Strat, don't want a second guitar to manage right now, and frankly I'm finding this tone experimentation fun!