Yet another thing to be aware of is that the Pacific Surfliner doesn't just operate between LA and SD. Some of the runs start/end farther north, in a few cases as far north as San Luis Obispo. So even if you are going to be boarding the southbound train at LA Union Station, there may be a bunch of passengers already occupying seats, who boarded farther north and are continuing south.

Also be aware that the best scenery (IMO) is between San Juan Capistrano and SD. That is the coastal portion of the route, and you will not see the beach constantly, but rather intermittently. (Just set realistic expectations. )