Genderswap pics like this one make me wonder sometimes... would Yuuno get so much hate from the yuri fans if he was a cute little meganekko, or would she still get bashed for being an alternative to NanoFate?
Given how fanatical some hardcore yuri fans are, I have little doubt that Yuuno gets a fair bit of flak for being a potential heterosexual option for Nanoha. However much as some Yuunoha fans might like to believe otherwise there's also a fair number of people who simply prefer NanoFate because they find NanoFate more interesting and compelling than Yuunoha. I know I personally don't see myself being inclined to favor a Nanoha X Female Yuuno pairing over a Nanoha X Fate pairing.
If Nanoha had gone with Yuuno I can almost guarantee that Nanoha would have faded away as just another magical girl anime. As ZK296 said the added yuri makes for a very interesting development, and they do it well with heavy subtext and having the fans go yes they are a couple but always having it done in a way that its not completely final. Yuuno faded so fast ionce he returned to human form.
Yuuno should have stayed a ferret pet >_> I love NanoFate from a yuri perspective and a normal relationship perspective. They're my favorite couple and Fate alone is just my favorite of everyone and everything.
At the moment though their relationship isn't clear, but they are both mothers to the same child. Much more interesting plot possibilities on that element than Sailor Moon or CCS because of that. And face it, Pretty Cure has a decent possible yuri element but it's more shoujo, less actual plot movement, and not as exciting, but more comical.