I don't think I've heard that. Do you mean complaints that iOS should be more like Android and not require all software go through the App Store? I've definitely heard that complaint. (And made it, at least on general principle.)
If not all apps have to go through the Apple App Store and multiple App Stores are allowed that are controlled by third parties (ie: not Apple,) what makes you think those stores would be ad-free? Simply put, I think that having multiple app sources naturally leads to ads in the App Store space.
Mind you, I hate ads and am in no way arguing in favor of them.
Nothing makes me think that. :) I just don't understand what's better about the Android App Store, unless it's ad-free. (Which would surprise me, mildly, given Google's core business!)
I don't know about Google Play, but Apple's App Store has absolutely horrific search. More often than not, I am googling the app name then finding the App Store link from Google Search results