They both suck on a whole but have their moments of brilliance.
Pretty much any genre of media is going to suck as an average, so that's a pretty pointless thing to say. There's a lot of really bad anime out there, and there's a lot of really bad Science Fiction out there, but neither genre invariably qualifies the content as "suck".
Anime is just a term used to describe Japanese Cartoon Animation. It's really just a culture-based art style used to portray storylines. The content of the storylines is what I'm really interested in. I tend to totally disregard animation style as long as scripting and acting are good, unless the animation is just completely botched.
Science Fiction on the other hand is a method of storytelling which I think is not only intriguing, but a great source of technological progress for society. I think that a story which is capable of stimulating the mind and generating productivity is extremely powerful and valuable, especially in our uninspired and monotonous modern lifestyle.
As an unrelated note, I don't consider Star Trek or Star Wars (or other such media) SciFi by definition because they're illogical; the underlying principals that act as a foundation for their story is scientifically inconceivable. I'd consider them Tech Fantasy. But I guess I'm probably the only one who holds to such an anal nomeclature and obsolete denotations when the social connotations are so vastly different, so I'm not really going to argue in favor of my stance there. I just want it to be known that when I say Science Fiction, I mean, literally, fiction based on science.
Also, because Star Wars allegedly took place a long time ago in a galaxy far far away, wouldn't it be Historical Fiction? ;]