I have visited a few times San Diego zoo during a short stay in Southern California. From my European zoonerd point of view, I very much envy the richness of gazelle species maintained in AZA zoos and with its dry climate, San Diego have perfect conditions to house them.
I would suggest that the current Urban Jungle and koala exhibit is revamped for an area based on Horn of Africa in the immediate continuity of Africa Rocks and hamadryas enclosure and kopje.
The area could be used to house a couple of lions in a better exhibit that the one from EO, maybe with a view on the canyon behind to create a scenic background and providing an endless perspective and stuff to look at for the lions.
This area could also house other jewels such as gerenuk, Soemmering gazelle with girafe (even if reticulated would be better suited than masaï), or maybe even/also Eastern black rhino. Speke's gazelle and lesser kudu should be also part of the stocking and having one or two extra Grevy's zebra stallion should be doable as well. I will not extend smaller species but I find always nice to have some kind of alternance between large and smaller species.
I struggle to measure how much space Urban Jungle would have to offer, maybe not enough for everything I mentionned but as much gazelles as possible need to go there !
The Bear and Cat canyon beginning should then be used to rehouse koalas and then continue with a South-East Asian theme. Enclosures for Malayan tigers, Malayan tapir with asian otters (or chevrotain), fishing cats could be created an the footprint of the Sun Bear forest and old grottoes. I do not remember well what other species are exhibited in the Tiger trail but I remind this part appeared outdated to me. Sun bears have no future in AZA so once they die, no need to replace them. On the contrary, the current monkey's exhibits that appear to be well suited should be kept. However, I am unsure of what monkey specie would be the best fit.
If I recall well, the meeting point of center street and Africa rocks trail used to have also large hornbills aviaries. I love these birds and I would be excited if SDZ choose to put some efforts in breeding them. With the unmodified orang-utan enclosure and Owens Aviary, that would have the potential to create one of the nicest Asian area in a zoo.
The Tiger trail being emptied of its Asian inhabitants, it could be used to extend the tropical African theme. One idea would be to create a newer ape facility in the canyon. I know this may be the less consensual of my suggestions but I found the ape exhibits okay but nothing extraordinary by today's standards. I have really no idea of how that would be feasible but imagine a large aviary full of vegetation with the group of bonobos being wtached by visitors at several meters height thanks to the natural inclination of the area !
The free bonobo exhibit could still be used, maybe for a gorilla bachelor group with some guenons mixed.
The Northern Frontier definitely need a refresh and polar bears to be phased out. I like the idea of housing grizzly bears instead and focus on local species but the California sea lion and seals addition would be a big mistake in my opinion. You just need to go to la Jolla cove, 15 miles from there, to see wild specimens accepting very close proximity ! (will add my photos from there someday)
Add the fact that pinnipeds are very hard to house properly with space and depth needs that are rarely met in captivity.
SDZ does not have a proper South American area and that is okay. Species are spread between the Children zoo, the Parker aviary, few monkeys in the mainly African Treetops way and several species on small sub-standards exhibits in Elephant Odissey. Maybe that could be another option to replace the Northern Frontier ?
In a more simple version, a large naturalistic enclosure could be created to house Baird's tapir with black-handed spider monkeys where the pelican lagoon currently stands. With the proximity of Ornate Hawk-eagle, and Harpy eagle, a small Central America area could be created. I do not remember how much space there would be left to extend this thematic.
Finally, the ungulates enclosures in front of the Last Frontier look to me like a nice place to do some nice enclosure for spectacled bears. The habitat could be some kind of dry forest (after Chappari Reserve in Peru) rather than the usual paramo or cloud forets habitat that may struggle from the heat up there on the plateau. I am not familiar with other Andean species that could complete this theme but please, let's avoid south-american camelids that are of no conservation interest !