Absolutely agree with the OP - Terminal E at BOS is a total garbage experience and mess for DL flights.
Domestic to Intl isn't too bad, as others mentioned DL at least has an airside shuttle from A->E even if it is slow.

Coming back Intl to Domestic is just horrid. Baggage delivery at BOS is bad on a good day. They almost always ignore SkyPriority tags and takes a significant time for bags to even start showing up. If you are coming from an eligible location, its basically a guarantee that you can claim the 'bags on time' 2k miles.
Signage - bad to none for what to do after you get your bag and leave customs. Best bet is to either go upstairs to ticketing and recheck your bag there, or walk over to A and recheck your bag there. Or just carry it on if you can as OP mentioned. Bus service from E->A is basically useless as it is landside, and you're better off walking along the connector through the garage. Its a 3rd world experience whichever method you take.

I'm not really expecting things to get any better when the E expansion opens either... it will just make the gates that much further away from the garage connector to A. The only good thing about the E expansion opening some time later this year, is the new SkyClub.