As a frequent tourist to SD with a need to ration my riding time, I offer the following suggestions:
The must-ride segment is the Blue Line from America Plaza (the downtown common point) to Old Town, then the Green Line (I think -- I don't have a map handy) at least to El Cajon (and beyond to Santee via the Orange Line if there's time; however, the frequency has been half-hourly beyond El Cajon, and there are better things to do if you're short of time). From the Amtrak Station (still called the Santa Fe Station, with the historic sign on the roof) you parallel the Amtrak Surfliner line, with two main tracks as far as Old Town, shared with the Coaster trains to Oceanside). There are a few common grade crossings, but the two major ones are grade separated for the trolley but not for the railroad, the trolley line having one overhead and one undergrade bridge. To the west just short of Old Town you can see the wye that was once used by the ATSF to turn the San Diegans prior to arrival at San Diego (apparently the schedule was too tight to head straight in to the station and then wye the train and back down to the station -- you can't get that mileage today). Beyond Old Town is (I believe) the only trackage on the system (to Grossmont) that is "greenfield" right-of-way as opposed to former (or surviving) railroad. The trolley operates for awhile on a concrete trestle required to protect wetlands, then traverses a golf course, with high wire fencing on both sides to guard against stray hooks and slices, then, after passing Qualcomm Stadium, with provision for special-event services that are heavily used (Coaster and the trolley jointly promote connecting services to sports events, with passengers changing at Old Town). Next comes a hillside right-of-way high above an 8-lane freeway, followed by a plunge into the hill itself and the only subway stop on the system, underneath SD State University (or UCSD, I forget which). You then emerge from the tunnel to parallel the freeway some more until the Orange Line (formerly a branch of the San Diego & Arizona Eastern, over which freight service is still provided) joins at Grossmont. Depending on time, you can continue to El Cajon or change there to go back on the Orange Line.
The second most interesting (in my opinion) is the Orange Line from America Plaza to El Cajon. The street running at the downtown end is kind of boring, but after it ends at 32nd St. (or Ave.?) there is a horseshoe curve to get down an escarpment. Next you travel between a couple of cemeteries before climbing back up to the original elevation or higher, with some nice curves, joining the newer line at Grossmont. If you do ride from El Cajon to Santee, the trolley line has a bridge over a major intersection requiring a gradient too severe for freight trains, so the original line still crosses the intersection at grade (I suppose once a day) to accommodate the covered hoppers.
Another interesting stretch is the rest of the Orange Line from 12th & Imperial to 12th & Imperial via 12th St. and C St. to America Plaza, running along the hypotenuse of the downtown triangle back to 12th & Imperial. That part parallels the freight trackage to National City. BNSF has some freight action on that line, but I don't know the details.
The original line (now the Blue Line to San Ysidro) has the historical interest of having been the first, but I would say that if your time is limited, it is the most readily expendable. One element of interest is that in rush hours, the trains are lengthened to four cars (!) beyond 12th & Imperial because the street trackage downtown will only accommodate three.
That's my take on it anyway -- good luck with the trip.