Remember how Kraft became a major player in the New England sports scene in the first place: Land. He bought the Foxboro Stadium parking lot, which he leveraged into buying the stadium, which then allowed him to leverage the lease in order to buy the team.
He owns Gillette and the land it's on. As great as a SSS in Boston proper would be, Kraft doesn't have to do that to maintain profitability and just as importantly, control. He'd have to lease out a plot of land in Boston for no small change, then get funding for a stadium while having to satisfy the zoning regulations and building codes that the city would put on him (likely much more strict than those he faces Foxborough), etc. In his little kingdom at Patriot Place, he can do almost anything he wants and doesn't have to buy land to do it. Nobody understands the value of owning property and land in sports business better than Bob Kraft. I doubt you ever see a SSS in Boston unless he gets an absolute sweetheart deal. Theoretically he could build a more intimate soccer stadium in the same complex as Gillette, but it's not something he needs to do as long as he's got the big stadium there that has open dates.