[ska]

"Now if we want to apply to YC post-pivot, we get penalized? That seems incredibly unfair."

I don't think that's what is being said. You say YC would not have accepted you in 2013 - what you would want to do now is be accepted in 2016 as a company years further down the road. Is the bar higher? Sure, but that's natural. Demonstrate that you've made good use of those 2 years and you are in good shape to proceed and you should be fine, is what I read into it.