New York-Boston

The numbers look compelling: Acela from New York to Boston takes about 3:40. One of the airline shuttles takes 1:05. Clearly, therefore, if you're in a hurry, take the shuttle. Not so fast...

Let's look at door-to-door, assuming downtown to downtown:

(I apologize for the formatting; somewhere I'll figure out how to get this in tabular form. Even with entering spaces, it compresses them for some reason. No, I meant to type those spaces! Sorry.)

Acela Shuttle
Time to terminal 0:15 0:45
Time before departure 0:15 1:00
Time en route 3:40 1:24
Time to destination 0:10 0:45

Total time 4:20 3:54

In a best-case scenario for each, the shuttle is only about 20% faster. If you have to check your bags, you're now talking about virtual parity.

Then let's starting adding in subjective factors:

Hassle factor Very low Have you flown lately?
Likelihood of delay Low LaGuardia...5 p.m....weekday...
Impact of weather Low Hotel room
Leg space Spacious Specious
Food It's not Lutece It's not at all
Fare (5 p.m. same day) $150.00 $339.50
(And for $68 more, you can get first class Acela that includes meal and unlimited cocktails)
Work ability The whole ride 23 minutes
Noise Quiet car Why you paid $300 for Bose

Tell me again why you're taking the shuttle? See you on the train...