I travel to Seattle several times a year...Its really a fantastic city. There are all sorts of things I would recommend, but if you're only going to be there for 2-3 days, I would stick to the Museum of Flight and the EMP.
I was at the EMP in August, with my dad (and if you haven't figured it out yet, my dad posts here as Charles802). Anyway, I was very impressed by the museum. The exhibits were not at all "flat" like in most museums, thanks to the the hand-held interactive Music Experience Guide "MEG." Some people think the Gehry designed structure its a bit of a monstrosity, and it is very expensive (19.95 is regular admission, including the MEG." We were unable to see the entire museum in slightly under 2 hours, so we decided to become members. The lines to get into the Hendrix exhibit were too long. I hope to return sometime next Spring. Even my grandmother became a member, little good that it did her
The Pacific Science Center at Seattle Center is also well known, although I haven't been there in years. The Space Needle has been remodled, but its pretty expensive to go up, and I really don't see the point.
I was at the Museum of Flight in June. I've been there four times, so I don't have much interest to go anymore, but the exhibits are great. The older "Red Barn" has a great history of aviation, and I believe it was one of the original Boeing buildings. The newer hall has a great expanation of the Air Traffic Control system, as well as many actual aircraft and a gallery on space exploration. An Air Force One 707 is also open to be toured.
The only hotel I've stayed at in Seattle is the Westin downtown, which was fine. Doubletrees up in that neck of the woods are old Red Lions, and I always recall Red Lion's having very spacious rooms. But, I've never been to that actual property.