There are only a few "rides," Sea World in San Diego is mostly shows and walk-throughs. Manta opens with the park and will develop a pretty good line later. We rode it several times in a row the first hour almost walking on last summer on a July day. Journey to Atlantis will develop long lines, but doesn't always open right with the park, so check at the gate before racing over like we did! The raft ride will be long midday as it warms up. The Skyride over the bay also doesn't open right away and will have a line when it first opens, but I don't think that line stays big once they get through the backlog waiting at first. The Wild Arctic simulator ride can get longer. We didn't do Riptide Rescue but it looks like a slow loader.
If I were putting together a one-day plan in warm weather, I'd probably do like this (check times guide for the later openings):
1. Manta 2x
2. Wild Arctic, walkthrough, and penguins
3. Journey to Atlantis (hour after opening?)
4. Raft ride before it gets too hot
5. Skyride
Weave in walkthrough exhibits, shows, food etc. It's hard to do everything in one day. If I could't fit in all the shows, I'd focus on the impressive ones -- orcas and dolphins -- and the sea lion show is quite cute too.
PHXscuba