The "I-5" (to the Fairgrounds) route is essentially the same alignment proposed by American High Speed Rail back in 1980. This is the route that seems to have the most public support, with the least technical or political "problems"... It is about as long a the current routing, but able to operate at speeds of 110 or 125 mph. on a full double track high speed main, instead of the 25-30 mph. now, on the single track 1882 alignment...
The "direct" alignment is a bit shorter, but through some very problematic geology, with some potentially expensive "ground water" issues, and made even more complicated, by the likelihood of arousing a lot of Nimby politics.
And frankly, the Coast alternative is there largely because someone would ask, so you have to say we looked at burying it along the existing routing...
Local CBS affiliate on Del Mar rail tunnel
San Diego UT story on Del Mar Tunnel alternatives....