The exit ramps at Haymarket are pretty bad, but the North End in general is one of the best examples of what a great project the Big Dig was and a great example of why you'd do a project like that in any city. So not really sure how you could say it's not really knitted back into the rest of the city.
I'm with you. But maybe the distinction is that the Bullfinch triangle section is doing very well - and it's because this is where we've actually put buildings on top of the thing, and put (kept) small streets on the surface. As we all know, buildings and small streets are what we mean when we say 'knitting the city together".
The north end section is different. The parks are very pleasant and well used, but if building and small streets are what do knitting, parks and big streets (and parking lots) are what do unknitting. The chasm between haymarket / blackstone and the north end is still a chasm, even if it's a vastly more pleasant chasm. To be sure a pleasant chasm can be a nice thing to have, but a lot of that depends on whether it has good knitting all around it.
That's why the north end ramp parcels are such a disappointment. The root cause here though is in the structure of the parcel. With surface streets touching the parcel boundaries on all sides, there's no terra firm for a core, and no interface space for loading & unloading people and goods (let along staging construction). This is why its too expensive to build there.
Its the same problem as with the Pike. Columbus center almost made it work with those small spandrels on the side of the pike, but ultimately it wasn't enough. If the city wants to get buildings in those places, its going to have to change the parceling and realign the street grid.
For the north end, doing this would have to mean taking a portion of the small block under the garage, realigning the through traffic to congress, and making the current street space and the bus area at haymarket part of a single parcel with the ramps. For the pike, it probably means building a new boulevard centered on (and cantilevered from) columns in pike mediuan, putting building cores on the current surface roads, and then cantilevering part of the buildings over a couple lanes of traffic - a hybrid deck, in effect, that combines street surface and building structure. Much cheaper in the long run than trying to construct an entire building suspended 10 feet in the air, and then trying to keep it there and service it for 100 years. (And i recognize that we discussed and mapped this prospect extensively a few months ago)