No need to blame Ian for something already chiseled into stone, you could say.
I don't think there was ever a problem if it was just a plot device, that is to be expected. Goes to the same point as to why Eggman could reshape the planet into separated dimensions with one emerald, dried up all seven to slice the planet into large pieces, or destroyed stars with no chaos emeralds at all. The power and abilities of the character will fluctuate as they always had, it's just that in the past this was just a plot hole that likely had no deeper thought from the writer at the time.
As far as I know, the reason could have been that they wanted to make the scene of Shadow slowing thinking about Maria on a rocket to the Ark, a scenario that couldn't happen with the same emotional beats as shown in the series if they just had Shadow chaos control to there.
At least to me, I'm perfectly fine with ignoring "what could have been as the most logical answer" if the emotional choice is good enough.
What really put Ian in a bad light, at least IMO, were his commentaries on the Bumblekast actively stating something that is known to not be true already a few times in the series. So accepting ignoring possibilities might be easier to do than actively denying a truth and using such denial as the explanation.
Ultimately to me, it doesn't matter how Shadow got there, I wouldn't trade the scene of Shadow thinking of a possible future with Maria for a 5 second scene of warping into the Ark from Episode 1 itself, sometimes lore will be bended or basically ignored to make for a good scene and I think every understands that, at least hope so. In the end, it's just the PoV of this long history of ignoring that stuff happened because "it makes hard to explain why they don't do that" that is a problem to me.
Of course, some people will just hate anything on him because they are haters, sadly I think they'll never change.