Great choice! I’m from Seattle and miss it every single day. What time of year do you plan on going? Since you love both outdoors and the city, you will have a great time. The neighborhoods in Seattle are wonderful and full of great coffee shops, restaurants, and bars. They are so easy and fun to walk around in.
I definately recommend the waterfront–you can go to Ivar’s and watch the boats, visit the unique shops, and just breathe in the salty air. Then go up to Pike’s Place Market for sure. You could also take a ferry ride.
Discovery Park–it’s in the city (in the Magnolia neighborhood). It’s a huge park and you’ll feel like you’ve gone far out of the city. It’s great for walking around in, taking a picnic, etc…
Golden Gardens–it’s a beach in Ballard. You could take a picnic and enjoy your evening and watch the sunset. The sunsets there are stunning (if it’s not cloudy obviously). I don’t know if it’s still allowed, but we used to build fires on the beach there and it was the best thing ever.
I also enjoyed the Ballard locks (I lived in Ballard and it was my favorite Seattle neighborhood). The locks are fun just to watch the boats and relax. And, if the time of year is right, you can watch the salmon go through the fish ladder.
If you want to drive a little, a romantic place to visit would be Snoqualmie Falls. I’ve never stayed there, but the Salish Lodge would be a wonderful place to spend a night or two on your honeymoon!
And I 100% agree about the San Juan Islands if you’re able to get to them. They are my favorite place in Washington. If you don’t have time to go to the San Juans, maybe you could visit Whidbey Island. It’s also really beautiful and closer to Seattle.
I have so many ideas for you, but just one more for now. You could go Kayaking in Lake Union. It’s so fun and you get great views of the city and can paddle near house boats which is fun.
PLEASE feel free to PM me anytime if you have questions!