I agree with NGC's comment about allergies, but for the rest of the year (in no particular order):
1) The bus system can be frustrating in that to get from neighborhood to neighborhood you might need to transfer through downtown.
2) Despite being called a highly bike-friendly city, I've found the opposite to be true in many cases. Sure, the Burke Gilman is great, but only if I'm going on a ride just to ride or if I'm going to school (UW). Riding on the streets is another story, and frankly, can really suck. Streets in poor repair, cars and trucks who nearly run you over, and people who YELL at bikers even when they are riding perfectly legally are all dangerous.
3) As a nearly life-long Seattleite, I used to think that people were making up or overblowing the Seattle Freeze. However, as I've grown up and taken a "different path" than most people my age, I've found it to be quite true. People often seem taken aback by any friendliness and almost seem afraid when I try to make conversation. And I consider myself to be pretty introverted - I don't mean I'm talking to people on the street, but people in classes with me or who work with me. It can be pretty frustrating. That said, I don't hold them at fault - in the cases where I have broken through the barrier, so to speak, I've often realized that they're even more introverted or are socially anxious. Vicious cycle.