Juneau has great trails and the landscape is absolutely stunning (glaciers, waterfalls, rainforest, great kayaking, etc)...however it rains about 3 times as much as Seattle i'm guessing...so if that bother's you then you'll hate it...personally I love that kind of weather with the fog rolling off the mountains but not everyone shares my sentiments.
I haven't lived in Anchorage but know the area well. Anchorage as a city is kind of a crap hole but the advantage is that it is a small city and will have a lot more things to do. The summer's can be pretty nice most years and it's not too far of a drive from lot's of great hiking and wilderness areas. Also, it's a lot easier to explore the rest of the state from Anchorage. Personally Juneau might be one of my favorite towns in Alaska but you might start to feel a little trapped if you're there too long.