there's a lot of misinformation in this thread.
to sum up before i get long-winded, it really doesn't matter if you are not hitting the red lights on the input meter. the Axe-FX II input settings only optimizes the signal-to-noise ratio.
from the wiki: "Note that the Input Level setting DOES NOT AFFECT GAIN, It optimizes the signal-to-noise ratio only. This is different from the Axe-Fx Standard/Ultra."
the OP says he "felt something missing" from his tone, but the Input settings will not contribute to that "something missing." only extreme high or low settings of the input gain will affect actual guitar tone with the Axe-FX II, and by extreme i mean the input lights barely lighting up at all or the red light on constantly. otherwise there is a HUGE useable range of the input adjustment. in my opinion, as long as the 2nd light is always lighting up as you play, there will be no difference in tone between that and the 3rd light always lighting up as you play.
Input trim does not affect the gain at the A/D conversion level so does not have any effect on the input lights.
sorry but part of this is absolutely incorrect. the input levels set in the I/O menu definitely have an effect on the input lights. that's exactly what those input lights are measuring.
I do use Noise Gates on most presets, so I'll try disabling those and see if there's any difference.
noise gates have nothing to do with the input level/lights never reaching red. the noise gates come after the input stage and input meters. it is possible that the noise gates are affecting your tone in a negative way though, but again nothing to do with input levels. not sure if the difference you referred to was a difference in overall tone or a difference with the input meters.
Also you can tell if your in left only if you look at the lights that light up when you hit a string. If both l and r lights are on you need to check your settings.
just echoing that this statement is not correct at all.
For those who easily push into the red - what do you attribute this to? Guitar, pickups, how the Axe is setup, something else? I'll need to check my I/O settings!
hard to say, as i only have duplicates of the same guitars (Music Man Petrucci models). on all my guitars, my input gain is roughly at 30%. around 40% the red input meter light comes on when strumming hard, then at about 60% it's on when playing medium/hard. yet, even at 100%, the tone is mostly unaffected, as the red light indicates -6dB (so 6 away from clipping).
some people have heard a difference in tone when they crank the input volume to 100% and cause the red light to come on all the time. what's happening is that the Axe-FX II is is actually starting to compress the input signal to help prevent input clipping. this compression may be mistaken for "better tone" but is fundamentally incorrect. if you want compression, use the Compressor effects blocks available, don't ruin your gain staging.
this whole conversation is only for the Axe-FX II - if you are thinking of or comparing to the Ultra or Standard, the input gain was very different and could affect actual gain/tone levels.
it has been prescribed that we should set our input level for our loudest guitar for the best signal to noise ratio, then leave it set that way and all other guitars should sound just as great. with a real guitar amp, you can't adjust this anyway.
if you feel that there is a substantial tone difference among different guitars and input level settings, i guess it's something you'll have to remedy and deal with. i don't have the solution. many people don't experience any differences or problems.
however, regarding guitars never making the red input light come on, it is not an issue by design and will not affect your experience creating tones with the Axe-FX II. setting your input to 100% and never clipping is ok by design.