Lets see...archaic ticketing system with poor transfer to subway / bus system
Well, the Commuter Rail is basically a completely different network from the Bus and Subway systems, so that would explain the "poor transfers" between them. Also, I know I may be in the minority here, but I really don't mind the Commuter Rail's "old fashioned" ticketing system of collecting tickets onboard, after all it is Commuter Rail, not transit.
Trains that sit for 10 minutes waiting just outside South Station.
This happens because trains often need to wait for another train to leave the platform they are due to arrive at, and they usually cannot just go to another platform because of the lack of capacity at BOS, this is why South Station expansion is necessary.
Crappy single track side platforms with bus style shelters for sixty years while they build Taj Mahals elsewhere
While I do agree that there are some real dumps on the system, the modern MBTA standard of Commuter Rail stations is not what I would call crappy, the seating is often enough and the shelters are more reminiscent of old railroad shelters than bus stops (as if bus stops even have shelters

). Look at the Old Colony lines for example, the stations on those lines are quite pleasant. The only "taj mahals" on the system are the century old historic railroad terminals.
platforms that are high level, then low level, then high, high, then low and they wonder why dwell time is high and fare collection is low.
I agree with this, the MBTA needs to step up and make all stations accessible, mini-high platforms should really only be in areas where there are wide Freight trains going by daily and building a siding to act as a passing track is not feasible or possible.
When I was taking the Commuter Rail there was a total lack of communication of information about delays to the passengers.
This is likely because most of the stations on the system have no staff stations anywhere, but with the addition of LED displays and information boards to stations, this problem will likely begin to fade.
T improvement projects that take years and years and are always way over budget. Does this apply to Commuter Rail or is it just the transit projects?
I honestly couldn't tell you, the transit projects are mush more common than the Commuter Rail projects, the last time a major Commuter Rail expansion project was being built, this was the case (Greenbush), but that was mostly due to NIMBYs and additional infrastructure built to appease them. I guess we could wait to see how SCR turns out.
Photo by Alan Thomas: NYNH&H I-4 Pacific #1372 proudly thunders through Forest Hills as it makes its way to Providence R.I.