Yeah, the 2mile sign is rarely implemented for any exit other than a major one. (ie another interstate).

Maybe there. If you don't believe me I'll drive into Pittsburgh after the snow finishes and take pictures of every interchange for you on the way in. The Penn-Lincoln Parkway East is definitely an urban interstate. The exit sign spacing is only substandard where the exit spacing itself is.

As to your later point about colocated highways...
Parkway East is I-376/US-22, and from Forest Hills inward, also US-30. The Parkway West is I-279/US-22/US-30.

As to the quality of signage in general - in Massachusetts they are poor. I think that's a symptom of other issues.

I think this is your actual problem. There are standards, Massachusetts may just be failing to apply them.

As to dual 128/95, 95 was supposed to go through Boston, but (arguably correct) NIMBYs precluded it. So now there are greenways and colocated 128/95.

And as to route 28 on the Cape, if I'm on route 28 north I should end up going through Medford and on north. Do the spray-painted corrections fix that, or more likely, do they break it?

There is rhyme, and reason; In some cases it's just poor.