I have lived nearby and used the local lakes for quite a while. I find Lake Union and Lake Washington to each have a very different character. Lake Washington is big, almost 20 miles long by 1-2 miles wide, and virtually surrounded by houses, which for the most part look a lot a like. For such a large lake, there are very few protected bays or estuaries to explore, and a limited amount of public access shoreline. Seward Park in the south is nice. But otherwise you are mostly in the big water. There is also no speed limit on Lake Washington. I was once caught off guard when i was hit and flipped in my kayak from a boat wake coming in from the rear quarter. Had I been paying better attention, like a pilot, I would have been looking around more, and also if i had better bracing skills, i probably would not have flipped. I enjoy going up the Sammamish Slough at the north end of the lake.
Lake Union still has remnants of the working lake it once was. Still a few dry docks dot the shore. More working boats can also be seen up into the ship canal and Salmon Bay towards Puget Sound for some good kayaking exploring. With the many marinas and houseboats on Lake Union, there are nooks and crannies to explore in paddlecraft. Except for a couple speed test lanes in the middle of the lake, there is a 7 knot speed limit on the entire lake, so it is unlikely you will be challenged by big wake. You need to keep a look out more for sailboats and the frequent seaplanes that drop in nearby in fairly close quarters. The pilots have it handled.
The Mountlake Cut is the cement trough that is part of the connection between the lakes. It does not take much extra power boat speed to create quite impressive confused seas, with all the reflected wave action off the walls. Probably best not to attempt it in a paddlecraft on a busy weekend afternoon, especially late in the day when the big boats are headed back to Lake Union for moorage. Other times would be fine. Don’t stop halfway and have lunch.