Well, I do think Anakin respected Qui-Gon more than Obi-Wan (yes, he had respect for Obi-Wan, but to me, it clearly wasn't on the same level). Qui-Gon also seemed more inclined to go up against the Jedi Council for anything he thought they should do (or not do), and I feel like he would have done that for Anakin as his training progressed. Now, I can't say for sure how much difference it might have made, but it does seem possible that it might have made enough of one.