OK, wow. Had I seen this thread earlier, we could have avoided all this.
To the original poster: W.A.D. - Works as designed. It's a technical phrase, I'll expand on it.
One should only expect what Line 6 designed for the Helix. By your words and expectations you are looking for a "amp/cab in the room" sound. Not gonna happen, nor does Line 6 claim it would. And experienced folks don't expect it. Sean Halley talks about this in more than one video that Helix sounds like you're in the control room and the amp/cab is in the studio. Hey, there's something to that.
Just ask Pete Thorn: http://www.premierguitar.com/articles/23115-tone-tips-modelers-versus-traditional-rigs " If you are used to hearing an amp “in the room,†going to a modeling rig can be a difficult transition. This is because guitar amps interact with the physical space they are in, and the resulting sound you hear [from the modeler] is the sum of the amp, cab, and environment. Many folks run their modeling gear into full-range, flat-response monitor speakers (aka FRFR rigs) that are placed onstage or close to them in an attempt to recreate the amp-in-the-room feel, but in my opinion, it’s a considerably different experience from having a cranked 4x12 behind you and flapping your pant legs." He's talking about you!
So, works as designed, I guess, move on as you have....