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The MBTA system is great and all as long as you live along certain subway lines within certain parts of the city, but I would give it a pretty poor grade otherwise. So if you can avoid the commuter rail situation, I would since it really sucks... especially going outbound in reverse traffic. I don't remember what time the interviews start, but realistically there's only 1 train that you can take in to get there before 9am. That would be the 6:50 am train out of South Station that gets to Grafton at 8am. The next one won't get you to Grafton until 10:30. Personally, getting ready for the interview and taking whatever train from the hotel to South Station by 6:30-6:45 (or heaven forbid, straight from the airport) would be stressful as all hell. If you absolutely have to take it though, I'm pretty sure you can call the campus police and they will pick you up from the commuter rail station if it's a yucky day or it's super cold or the street is not amenable to walking in pretty interview clothes. Here's the schedule if you want to take a look. Gross.
Taking the commuter rail + T fare round trip is going to cost $24-25 too, so it's not exactly cheap. If you can share a rent a car with someone, it might be REALLY worth it. The Boston area has a ton of zipcars, so if you're a member that's actually probably the best deal you'll get. That's how I got to my interview and back when I lived in the city. At $7/hr and not having to pay for gas, it really couldn't be much better.
I definitely agree about the terrible schedule. It's one of the reasons I drove to Boston in the morning at 5:30am rather than taking the train.