Too many walls of text here, but here's my take on things here:
North-of-the-Charles Urban Ring *at this time* must be a DMU and South-of-the-Charles Urban Ring pretty much has to be a subway. This is the ideal balance of current operational ability and capital investment. BRT applications are incredibly limited, particularly in Boston. SLG in Chelsea is a great starter, but again, a limited application. Widespread use of "BRT" will be anything but the "RT" portion -- it will kill off the project, "See, look how poorly it performs and it doesn't meet ridership expectations!"
North-side is easiest to tackle. Why use a mode which has to be segregated? If you're going to have a four-track ROW from Sullivan Sq to Chelsea, imagine the flexibility of mixing DMU's with commuter rail on four tracks versus commuter rail limited to two tracks and subway limited to two tracks. It also doesn't screw with the Coke Works freight in Everett.
1) Because on RR mode the train--any train--gets 100% of the priority through grade crossings, and this is what kills the frequencies on the Grand Junction. If you had BRT or LRT, anything you run on the ROW can share traffic light cycles with the cars. This is perfect for Main and Broadway, because you just re-time a pre-existing light to insert a transit cycle and there is no adverse effect whatsoever to cars. On Mass Ave., still some problems, but enough of an improvement that you can hedge.
You can't do that as long as it's RR mode. Every movement along the tracks--a freight, a DMU, a T non-revenue lash-up--induces one full set of gate timings that can't be shortened or interrupted. At every crossing. So there's a sharp upper limit to frequencies before the effect on car--and bus on the 1 and CT2--queues becomes a worse side-effect than the cure. And it's probably a lot lower a frequency than they can run on any other Indigo branch. Which makes integration with the rest of the Indigo network at West and North Station dodgy because the frequencies are likely to trail all other Indigo routes by such a wide margin.
2) The interface around Boston Engine Terminal for north-to-south isn't equipped to handle this. You can't just take a bypass around the freight tracks and speed right onto the Eastern Route off the Grand Junction. It makes a royal mess of ALL northside rail operations to foul that many tracks. Not only does it maim commuter rail service reliability on all lines, but it imposes an even more uselessly steep cap on maximum DMU frequencies.
I suggest checking out the shouty RR.net thread on the Amtrak subforum about batty, foam-covered New York-Portland Downeaster routings that did exactly this around-the-horn dance of BET to skip North Station. And how many ops people chimed in detailing every single interlocking that would fuck up to impossibility. Impossible for ONE Amtrak round-trip per day.
There's a reason why nobody's studied exactly this type of intra-city use of track despite contiguous lengths of connecting track existing in the barest physical sense. It's the ops nonstarter of all ops nonstarters.
3) The key finding that came from the Worcester-North Station study on the Grand Junction was about frequencies, and while that was a conventional commuter rail study there's some conclusions in there applicable to Indigo frequencies and any notion of using Indigo on this particular corridor as a UR starter kit.
-- In the Worcester study travel time from to North Station with intermediate stop at Kendall on upgraded track was more or less a draw vs. to South Station with intermediates at Yawkey and Back Bay. Couple minutes longer on average. Grand Junction's sharpest curves and extra coasting time required in the northside terminal district for the funneling into the drawbridges gives southside a slight advantage.
-- The NS direct generated its most demand at peak hours when Orange from BBY-NS and Red from SS-Kendall were at their crapshootiest and most unreliable. That's probably even more true today than it was 5 years ago. Demand was pretty convincing.
-- Demand fell off the table at all other hours when Red and Orange were no longer under load. Travel times BBY-NS and SS-Kendall on the subway were within the +/- 2-5 min. margin of error vs. a commuter rail direct (margin of error particularly coming into play at Kendall because Red and GJ are far enough apart for walking distance to vary person-by-person). Riders preferred to pool towards the subway frequencies the hours the subway was functioning like it should.
--
(This is where it starts to matter for Indigo...) Demand on the Worcester Line at all off-peak hours was
maximized by keeping the highest possible frequencies confined to a single routing, and let the highest-frequency transfers--Orange and Red--distribute the passengers. Rather than diluting inferior frequencies with one-seat forks.
What does this mean for Indigo?
-- If you're going to have a connecting leg on the GJ serve as a shuttle, mixer, distributor or alt. route scheme...it has to match the frequencies of what you're running on all the Indigo pieces it's connecting together. Otherwise passengers will opt every time for the subway transfer. So if the grade crossings impose a 22-25 min. ceiling on bi-directional frequencies vs. 15-18 minutes on the mainlines, that's 'THE' demand killer. Outside of peak Red/Orange rush hour despair people will opt for going straight to the terminal for nearest subway transfer, or (for Chelsea) straight onto SL Gateway via South Station.
-- It is worse to dilute anyone's frequencies for the sake of shivving in alt routings, so if some thru-routing from Allston to North Station dilutes to any degree service from Allston to South Station, the net result is going to be worse than if you just did all-trunkline, zero-diverging service. For same reason: Orange, Red, and Silver draw more all-day ridership the more they're all-day fed. Diverted trips to the northside hurt more than they help if frequencies aren't 1:1 compensated.
-- If the intent is to string it all together with thru-running on some northside routes for the 2024 map, the BET situation is a triple-whammy. Let's say for argument's sake that routing is even possible some of the time. Or reversing on-platform at NS is possible more-than some of the time. What's that peak headway going to be for "Indigo as proto-UR"? 30 minutes? 35 minutes? Now throw that on the pile of what we already know about frequencies GJ < mainline and see how this ends up answering a question no one is asking.
Frequencies matter. And that's why if the GJ isn't up-to-snuff on the RR mode for even providing the baseline frequencies all other mainline Indigo schedules can...it's going to be the very first cut from that 2024 map.
Also...fix Orange and Red, fix Orange and Red, fix @#$% Orange and Red. Because all the data points to doing THAT as the #1 "Indigo"-related investment that blows the roof off Indigo demand and utilization on the Worcester corridor and has the biggest cascading effects to all the other Indigo lines via Orange to the northside. Transfers that work are where you get it hauling some real butts in seats.