I felt the first season was weaker, but it got better as it went on. Initially, it fell too much in the standard Luddite mode of portraying scientific innovation as an evil that will destroy us all by Tampering with Things Man Was Not Meant to Know, with the only sensible person being the ordinary Joe who knew nothing about science but had Common Sense -- the kind of anti-science attitude that doesn't really fit science fiction. But it got mostly over that and became a show that celebrated scientific curiosity, portraying its cast of mostly scientists as heroic and the crises coming from unexpected interactions of worthwhile scientific endeavors. Instead of portraying the pursuit of knowledge as intrinsically harmful, it portrayed it as something that was worth taking risks for.
More than that, despite the fanciful nature of its science (and that got somewhat better over time), it was arguably much more of a genuine science fiction show than most, because it was fiction about science and scientists. A lot of sci-fi just tells fairly standard drama or crime or action stories with the speculative science and technology being mere trappings, but in Eureka, scientific breakthroughs and the work of science drove the narrative, created the problems, and provided the solutions, which made it science fiction in the truest sense.
My biggest problem was the intrusive product placement. It wasn't so bad when it was reasonable products for the setting like Cisco Systems phones or electric cars, but when they wrote a whole season arc around research into Degree antiperspirant and had it save the day in the climax of the arc, that was just going too far, turning the show into a commercial.