Staying in Old Town will be fine for the reasons you mentioned--connections to transportation.
For getting around San Diego on Day 4, I can understand wanting to use the Old Town Trolley hop-on, hop-off tour bus for a one-day visit. It gives a good overview of the attractions along the route.
But I have to admit that, as a frugal fuddy-duddy, I have a hard time shelling out $34 per person just to get around the city, when a $7 day pass ($2 one-time fee for a reusable Compass card + $5 day pass) on the San Diego Metropolitan Transit System's Green Line light rail route will get them to many of the same locations for a fraction of the cost. (The day pass is good for unlimited rides on trolleys and buses for the day it was purchased.)
When you look at the trolley tour map:
You'll see that destinations B, C, D, E, F, G, and K are all within 1.7 miles of each other. The Green Line gets you within a few blocks of each of those destinations:
- County Center/Little Italy Station gets you within 3 blocks of Little Italy (K) and the Maritime Museum (B)
- Santa Fe Depot Station gets you within 6 blocks of Horton Plaza (E) and 4 blocks of the USS Midway.
- Seaport Village Station gets you within a block of Seaport Village (C).
- Convention Center Station drops you at the Convention Center (BTW, the San Diego International Auto Show is at the Convention Center 1-5 January http://www.sdautoshow.com/ )
- Gaslamp Quarter Station drops you right at the base of 5th Avenue, the entrance to the Gaslamp Quarter (F)
Stops D and G on the route are stops at the Marriott and Hilton hotels.
Old Town Trolley Tour buses run about every 30 minutes from 9:00 AM to 5:00 PM.
The Green Line trolley runs every 15 minutes from 4 AM to 11:30 PM.
If the boys wanted to hit the Zoo or Balboa Park, they could hop on the #7 bus with their day pass.
Heck, with our major attractions downtown as dense as they are they can walk between many of these places. In October, I had some 60-something friends visit, and we walked from the Little Italy Farmer's market at India and Date Streets to the Maritime Museum to the USS Midway (1 mile) without a problem. I'm sure your boys could handle that if we could. :-)
Granted, by doing it themselves, they won't have the narration that comes along with the $34 Old Town Trolley Tour, plus they'll miss out on Coronado (unless they take the ferry over ($8.50 round trip). But, honestly, I don't see Coronado as being a primary draw for 20-something football fans despite its nice beach and upscale small town feel.
Riding the Green Line from Old Town to Gaslamp Quarter is quite safe, passing through popular neighborhoods.
If the boys are interested in a more structured tour, then the Old Town Trolley is definitely worth it. But if they're willing to walk a little and explore on their own (which is what they'll do once the bus drops them off in a neighborhood anyway), then I'd encourage them to give the SDMTS a try. (And, no, I don't work for SDMTS--just someone who's been finding out its value as I use it more and more.)
Edited: 12:47 am, December 19, 2013