That's been floated time and again for generations. Just like that cross-harbor interstate replacement for the Big Dig that certain quixotic groups of individuals keep flogging to this day (if not as a realistic build, then to say "I told you so"). It always gets shot full of holes and ends up looking really poor vs. the conventional Link routing.
-- You lose the ability to thru-route to every northside line except the Eastern Route. There is no capacity for backtracking on that dog-slow Chelsea jog all the way to Somerville--undoing nearly all the extra distance you've traveled--in order to feed Lowell and Fitchburg. Lowell Line is where vast majority of the thru-running ridership to 128 and other population centers is, and where the capacity suits it. This defeats it right off the bat, and now for all intensive purposes you've reduced your case to an airport connector in isolation. Which is not what run-thru regional rail should ever be distorted around.
-- The only viable RR tunnel trajectory from an underground South Station crosses the Harbor at the widest possible point and longest possible tunnel length at maximum possible expense. You can only deviate off the official N-S Link trajectory at about the Northern Ave. Bridge because SS Under is locked in place on only one alignment slipping between Red, Silver, and Pike tunnels. The Blue Line tunnel blocks the shortest hop across the water at Long Wharf so you can't hug the coast. And you've overshot Southie by the time you have freedom to move so you can't hug that coast. 1.2 miles corner-to-corner...that's how much tunneling you have to do for this. Almost 3x longer than every other crossing: Ted, Callahan, Sumner, Blue. At 4 tracks for equivalent capacity with the proposed Link, this will be one of the most expensive tunnels to build in North America. Much more expensive than the proposed Link because you still have to build exactly the same hard parts around South Station as the official proposal to get there at all.
-- Showcase airport rail connections have a bad reputation in this country for badly underperforming their expectations. It's a necessary evil to have
an airport connector, but overplaying its importance and attempting to alter the entire transit center of gravity in the city away from the CBD towards the airport is almost always a loser. Airports by necessity are away from the CBD and are more or less urban deserts devoid of anything except explicitly airport-oriented services. They have boatloads of TOD, but it's single-task TOD in direct support of the single-task airport. Trading all the destinations around North Station for all the destinations around the Logan Terminals is a ridership killer (compounded by the flaws of how much of northside commuter rail it cuts off or renders nearly useless). North Station frames one side of a fully-enriched, fully-diversified central business district. Logan is the antithesis of the CBD because of its single-tasking. Too many cities conflate the two and end up overinvesting in their airport connectors thinking "Well, it's a TOD paradise and people gotta use the airport!", not realizing it's a two-dimensional destination vs. the CBD.
-- Another reason why airport connectors don't perform to expectations is that the most frequent of flyers use public transit at lower rate than the general population. That's the luggage factor. If you're only an occasional flyer, yes, you're likely to use public transit at roughly similar rate as the general population. But it's the frequent flyers who bring in disproportionate airport revenue. If you are on the road a few times a month, lugging your stuff around through transfers gets real old real fast and your likely preference is going to be for private ground transportation. Any company that doesn't run itself on a shoestring pretty much makes ground transportation a default in its travel budget. It's a necessary price of doing business when hiring and retaining real road warrior employees requires taking some hassles out of the experience. Having the frequent flyers use the mainline airport station at several ticks lower % than the general casual flyers lowers the growth ceiling for that station to the point where it's unwise to overbuild it and doubleplusunwise to pass up the CBD for the airport. It needs to be right-sized to task. That's the single-tasking aspect of airport transit throwing some planners for a loop when they over-equate the airport with the CBD.
-- The one-seat convenience for
some people does not undo the limitations of the last point. Because not everyone is going to be doing a one-seat trip, even if the ones who do have a one-seat available to them use the service in droves. Not every destination even on run-thru commuter rail can be done without transfers. That includes car transfers. The hotel or the office park is not going to be across the street from every commuter rail platform, so the road warriors' utilization is still going to be lower than the population of casual travelers. With the road warriors' disproportionate influence over airports, the ones who do get absolutely perfect door-to-door transit service don't make up enough of the attrition from the frequent flyers taking a pass. Draw the station away from the CBD betting too big on behavior that isn't there, and that hurts more than it helps.
-- These lower margins at a two-dimensional destination are best suited for more of what we've got and what's been officially proposed: transfer-oriented connectors of moderate capacity and quick in/out travel times to the terminals. SL1 is an entirely appropriate airport connector. Actually, BRT in general hits a little above its weight when it comes to serving airport connectors than vs. some other applications where it's mis-applied because it can go door-to-door at each terminal in pretty nimble fashion while an HRT or commuter rail station can only feasibly make 1 stop at an airport that has to unfavorably split the difference between terminals. We can quibble with the final form the Transitway took and the lack of follow-through on getting to downtown, but SL1 is pretty good for what it does. Urban Ring LRT on the north flank would be very good for what it does as an airport connector...because it's all about transfer-to-transfer destinations, not overemphasized on end-to-end one-seaters, and links the CBD to a diverse set of other general-purpose destinations. Same can be said for Blue. It's a North Shore to downtown oriented route that just happens to clip the airport; the Airport doesn't distort the routing the one-seat rides use it for (which is also why a Blue branch to the terminals that siphons frequencies or capacity away from Eastie, Revere, Lynn is a lousy idea).
Some illustrative reading:
http://pedestrianobservations.wordpress.com/2013/09/30/who-regional-rail-is-for/
^THIS^ is basically why none of these harbor bypass proposals ever pass the laugh test. The center of gravity in any city is too heavily weighted to the CBD. Without North Station, run-thru regional rail doesn't pull its weight here. At all. There's no reinventing where the N-S Link goes. It can only go one place and still do its job. Thankfully, they provisioned for that when they did the Big Dig. It costs less to scoop out the fill under 93 than build a 1-1/4 mile bore across the Harbor when all else cost-wise around South Station is the same either way. Why would anyone opt for the latter when the ridership to the other side of the CBD so stratospherically better as well as the thru-running options to the northside lines that have the most thru-running demand?
Solution in search of a problem. And solution that ignores to its own peril where the real CBD-oriented driver for run-thru regional rail is.