As long as you are here after Labor Day (first Monday in Sept) the crowds go way down. School starts before or the day after Labor Day, so all of the children are back in school.
The weather is gorgeous year-round, IMO. The ocean temp won't change much; the air temp will be a little warmer than your original plan for October. If you are coming out of winter, you may feel the difference. There is less rain in Sept than Oct but still very little overall.
For
Disneyland, there will likely be several rides closed for much of September. Take a look at this list from this year:
Disneyland Monorail opening at 10 a.m. Monday through Friday until further notice. This shortened schedule is due to the Buena Vista Street construction in DCA. The monorail operates on a normal schedule on weekends.
Matterhorn Bobsleds closed through September 1 for refurbishment.
Haunted Mansion closed August 29 to September 15 for installation of the Haunted Mansion Holiday overlay.
Pirates of the Caribbean closed September 7 to November 23 for refurbishment.
Blue Bayou closed September 7 to November 23 for refurbishment.
Space Mountain closed September 915 for installation of the Ghost Galaxy overlay.
Mark Twain closed September 2628 for deck oiling.
California Screamin' closed September 6 to October 14 for refurbishment.
While the list will change next year (and the DCA construction will be mercifully done), September is a prime month to refurb after summer season and before the holidays. They also close the rides for their Halloween overlays during part of this time. If there are absolute must-rides, your likelihood of finding them under reno goes up during Sept. The plus side is that the crowds should be smaller in Sept than in Oct. The only possible problem would be if the DCA renovations get way off track and they are still opening things in late summer -- could spike crowds.
Read HydroGuy's
High/Low Season tradeoffs thread if you haven't already. October has rapidly become much more "high season."
As for the San Diego attractions, the off-season may mean shorter hours and closures, but not much difference between Sept and Oct overall.
PHXscuba