I'm finding this too.
I am a pod farm user from way back. I found it FAR easier to dial in a gnarly tone on pod farm than Helix. Granted helix has far more options etc, but it shouldn't be so hard to build a solid tone. I can't go back to podfarm, as I've upgraded to cubase 9, and it's exclusively 64 bit.
I'm finding that I'll spend hours on a tone, think it's "okay" then come back to the session only to hate it. it sounds "pale, scratchy, thin". Sure, it stands out in a mix, but it stands out for all of the wrong reasons.
I solely use USA PRS guitars (endorsement), and i'm not going to meddle around changing pickups. The pickups are fine. I've tried Helix Native with at least 7 different guitars with the same outcome.
I've found that the only way to get a semi-decent tone quickly is to couple helix with ezmix by toontrack. Honestly, i wish they'd just make a 64bit Pod Farm. :(