I also find their claim of needing to acquire all the properties - 19 more - before design work begins in earnest to be bullshit of the rankest kind. Yes, it was a problem for the Greenbush Line. But I don't see why design has to wait until after they own all the properties. It reeks of making excuses.
And they should focus work on what they can start now. There are all of five buildings anywhere near the ROW between the current viaduct and where the line crosses the Fitchburg Line, and I'm not sure how many of those (if any) will actually come down. (There's a lot of space currently occupied by gravel parking lots). So why don't they focus on getting those few properties, and then start on the work to get the line at least to Brickbottom (which shouldn't require much, if any property acquisition)? I mean, the only property to acquire at Brickbottom / Washington Street is a lot filled with old broken cars.
That's how this project is going to have to work, if they're going to delay it. Break it up into segments. Got the clearance for that first segment? Design it NOW, and get trains running. Got everything you needed on the Fitchburg Line? Good, design starts tomorrow, and the parts that could be pre-designed get shovels in the ground.
Time is of the essence? Then use the same tactic that worked on highway projects like the I-93 bridges and (in CA) the 405 work. Time-sensitive contracts: the longer it takes, the less the contractor gets paid - but they get penalized if they do shoddy work. Doesn't end up costing more, because it seems that the longer something drags on the more expensive it gets.
I assume that most of the property needed is for station projects, as they already own the CR ROWs. So if they're looking to avoid getting punished, maybe they should build the College Avenue station first and getting service there as soon as possible, even if it runs express from Science Park (or Lechmere 2.0). Make the other stations in-fills as property is bought up; use the time-variable contracts to get the work done on nights and over weekends.
Now, maybe that's not possible. Maybe they have to build the entire Phase 1 in one solid chunk. Maybe they really are doing their absolute best, and this is simply too hard to do before 2018/2020. But to me, it looks like they could be doing a lot more, and looking at some earlier-focused alternatives, on what is the number one extension priority (excepting Wachusett and Wickford, both of which are already in building).