If IE had 99% market share today, it would presumably have been because Microsoft's plan to proprietize the web was a success. Dependence on ActiveX, VBScript, and whatnot would have made non-Windows web gadgets technically infeasible.
I don't know about infeasible. It would've looked a lot more like the cell phone market used to. That is, you could leverage the internet to positive effect, but only if you controlled the front-end and the back-end, ala RIM.
And Apple could and did do that; albeit their branded services weren't adopted very highly out of the gate as people had choices.
