Project management or lackthereof. The T (esp. Commuter Rail division) has simply lost the plot at managing the nuts-and-bolts of station projects. Right down to repairs, which is why we've got a record number of closed-for-repairs stations at the moment.
The Reading Line would actually be a great slump-buster for getting back to basics. All of the stations excepting Reading (full-highs around the historic depot building is going to be a complex undertaking, but thankfully that one is currently ADA-compliant with the mini-high) are generic as can be, no architectural touches that need preservation, zero curves, no property pinches, and dirt-simple access points from a grade crossing (i.e. no up-and-over required). About the only halfway-tricky (but really not hard) one is Wakefield, since it would have to be flipped south of the Albion St. grade crossing to net T-regulation 800 ft. platforms. You could wad up all 5 stops south of Reading Depot into one project bid, and close them 1-2 at a time to blitz 'em, prefab the hell out of everything, and be done on a rapid construction schedule. Make it big enough that workflow efficiencies have to rule and project management bloat simply has no time to accumulate.