It's a problem with me and every media I ingest, really, and it can get in the way of enjoying things, but honestly, I think it just makes the experience better if you can accept that you like something as it is, even with its flaws.
My best example of this is Rin: Daughters of Mnemosyne. It's got a lot of strong points, but the flaws are sometimes glaring, and for what it's worth sometimes the art just kinda dulls out, or sometimes it will get a little dry and boring. Ergo Proxy has a similar issue with that. But, if you can examine things critically, you can also see what a show does well, and you can form a more educated opinion as to whether or not you like something and for what reasons.
My only challenge is when I try talking to people and I assume that they understand that you can like something that's flawed, especially when the conversation is about Sword Art Online or RWBY. I'm fine having a discussion about the flaws in the shows that I like, but so many people take it personally, like "no, how dare you say this thing I like is flawed!" or something. Meanwhile someone can come up to me and be like "Hey the art in Claymore really sucks and I can't stand to watch/read it because of it" and I'd be like "okay yeah the anatomy is pretty weird-looking."
The fact is exactly what you said: hardly anything is absolutely perfect 10/10 all the time, even the two things I stand by giving a 10/10 rating to (that is, GITS:SAC and Metroid Prime 1), and that's okay.