I think this isn't really true. 6% puts the base of the incline at 2nd Street in Chelsea. Note again that this is the
sea-level base of the incline; ground level will be higher, and the rail ROW will probably already be elevated at that point. So the actual incline could probably start a bit further south, which also helps ameliorate the cost of flattening the grade along the platform. (It looks like ground-level in Chelsea is about 20' above sea level in that area.)
I think 2nd Street is a perfectly good location for a station. If anything, siting a station slightly northeast might be better. You also wouldn't want to put the station that much further south, since your 10-min walkshed is already bumping up against the water.
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You do lose out on access to Admirals Hill if that's where you site the station. But, it's a hill (looks like about 85' high on the side near Tobin); diverting the ROW off the bridge for a short jaunt to a modestly elevated station might be feasible. But losing Admirals Hill isn't a problem unique to a Tobin alignment -- a Grand Junction or Eastern Route line won't get there either.
Charlestown, I grant, is a bit harder. In the above examples, I assumed 135' clearance over the Little Mystic, which pushes a station as far south as Prospect St, which I agree loses a fair amount of potential riders. That being said, the current Tobin has 100' clearance of the Little Mystic, which would only require 1670 feet running distance of incline, putting a station between Vine St and Bunker Hill St, which is better but not by much.
If you assume the station is elevated 20' (which doesn't seem unreasonable), you can push the station north of Vine St. At that point, I do think the walkshed is reasonable:
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And as you can see, we start bumping up against the water again, which means that siting a station further north actually doesn't get you as much as you'd think (though yes, Spaulding's presence is notable):
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Sorry for all the TED Talks here, folks. Like I said, I'm not married to the Tobin alignment or anything. But I feel like I'm operating on a significantly different set of facts than some of you, and I genuinely have that "Am I crazy?" feeling. Am I missing something obvious?