I don't want to sound to hard on the Seaport, but I can think of a few reasons Assembly has been turning out nicer, in my opinion.
Assembly feels a lot more pedestrian friendly. Basically everything is tree-lined. It's mostly wide sidewalks. There's narrow space for cars, so cars go slow, there's less traffic, it's quieter and easier to cross the street. By contrast, Seaport has a lot more wide arterial streets that are loud and less pleasant to walk around. Also, Assembly seems so much more dense with ground floor businesses. Each new building is designed to have that basically all the way around the ground floor, and most of the storefronts aren't giant, so there's a variety of things on each block. The Seaport has pockets of that, but a lot of the Seaport feels really sparse. A lot of the new buildings dedicate a ton of ground floor space to big lobbies (that no one uses), loading docks, and parking ramps. Those aren't fun things to walk around, so fewer people do, and the neighborhood ends up less lively. And also, Assembly is packing in way more residential above all that, along with office buildings. The more housing is good in itself, but also likely makes it easier for all those ground floor businesses to stay open later and for the streets to stay pleasantly busy more of the day. Assembly really seems like the closest we can get to the kind of urban density that hasn't been built in this country in 100 years. Seaport just isn't.