I think the problem is she isn't very good at maintaining herself or a smart schedule yet. She has even said she probably should have skipped some tournaments after the US Open. She definitely should not have played Tokyo and Beijing possibly. I don't think what Serena does per se has a negative effect on Vika. I am sure it hurt to lose in much the same fashion as she did the year before, but Vika is used to Serena by now to know that nothing is certain against Serena. You could be 6-1, 5-0 against her and Serena could claw her way back to a win. Every player knows this about Serena, so I doubt that weighs on their minds when they lose against her. If anything after the US Open, it should make facing Serena harder, not losing to other players. I think she just didn't really think her schedule through really, and wasn't mentally and physically at times ready to play this fall circuit.
I think the one thing you can maybe take as a negative for players like Maria and Vika is at their age this is/should be the prime of their career where they are winning everything left and right, but they are going up against someone who found a new level at age 32, so they are not. Serena has a hunger and goals now. She is in legendary status and building her legacy with every new win. That has to be hard when what is usually the decline age for women in tennis the 30's isn't showing itself to be true.