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.