Keep in mind you're moving to earthquake country. Most places in So Cal make sure that builders build "to code," meaning you're fairly well protected. But if "fairly well protected" is not good enough for you, you may want the builder to make the house better than code. On the off chance that he's bribing the inspectors (it does happen), you do not want a sub-code house. Not here. It's not likely he's bribing, but it does happen.
The place where the walls join the foundation (along the sill plate) is very important - the bolts (I think they're called red bolts) must be well embedded in the foundation - you need the proper amount of bolts - and they need to be the right strength.
Next is how the beams (and some studs) are joined. Normally these are just nailed together. But in earthquake country you want to additionally strenghten them with "ties," metal plates that get screwed on (and keep the joint from breaking, like simple nails would, in a shaker). They can be L or T shaped. For redundancy you can ***** and glue them on to important wood joints.
What protects 2-story houses is "sheer." Sheer is "stiff wall" that lends support to the structure when it's moving. Sheer grade plywood is used - you can ask for a stronger grade if you want.
The above will save you from many earthquakes. The idea is that the wood in the house will bend a little and move w/ the quake, but the important parts won't snap off.
Expansive soil. So Cal is practically all adobe clay, which is very expansive. The builders will put a lot of attention into the house's slab (the inspectors will, too), but make sure they don't ***** this up. They mustn't skimp on prepping under the slab. This means enough sand (sometimes it's crushed rock then sand) under the slab to "buffer" it from the expansive effect of moving clay soil. In summer the soil shrinks in the heat as it dries. In winter, when it rains, it sponges out.
Expansive soil messes up driveways, sidewalks, gargen walls, etc. Make sure you build well to head off the problems it causes.
As others said, go for heaviest insulation and best pipes you can.
Note where pipes are. Do yourself a favor and don't plant trees or shrubs with invasive roots anywhere near your pipes. Ask a nursery whether or not plants you intend to use are known to be pipe-invasive or not.
Do not change your plans mid-stream, if at all possible. The mark-up will kill you.
Is this a sort of deal where you pay and the builder builds your home for you? If so, they will cut as many corners as they can. It's how they make money. If they can save as little as $50 a house over 1000s of houses, it really adds up. See what your rights are. The gov't inspectors are your friends. The builder will hate them and will accuse them of slowing your project and messing it up. But they are the only thing stopping you from getting a piece of crap from the builder. Try to meet and talk w/ the inspectors. Any goof-ups should come out of the builder's pocket, not yours - don't let them shine you on this.
You'll have to be smart and tough. Builders are all part criminal and will try to get away with stealing from you or ripping you off in some way.
Oh, roofing. The wind can howl like hell in parts of so cal. You don't want a cheap roof - the tiles can be pulled out. If money is an issue, it's not that hard to fix. But a well-installed roof made of heavier material is a good thing, long run, if you can afford it. Avoid flat roofs and "rock roofs" (I dont' think they make them any more).
Back to concrete - if they do a ... gah, can't remember the name. They put tenstion on steel cables. That's a good, strong foundation - and - you know the steel won't be "stepped down." If they go w/ rebar, make sure they don't step it down. Steel reinforced concrete is only strong if the steel is IN the concrete. When they pour, they have to walk around in the concrete to spread it out and etc. And they step down the grid of steel rebar. They are supposed to feel as they are leaving and make sure the steels is up and IN the concrete. BUt many times they get tired and lazy and don't do it - "Oh yes ma'am, that steel is definitely in that concrete" they say w/ great confidence. Liars. How do you know if your driveway, foundation or sidewalk steel is in your concrete? You don't. But try. Ask the inspector for help. Earthquakes do much more damage to concrete where they steel was walked down - believe me - I've seen it.
Mostly, construction workers are lazy bums for the most part who want to do the minimum work necessary for the most money possible - and they just want to be done w/ it. Sure, some have pride in workmanship. Many have no formal training and have no clue. They will goof up something. The inspector will miss something. Just have some money ready for the ugly surprise. It's coming.
Try not to pay too much for the lot. RE prices are high right now. Make sure you can afford your loan if prices drop. If you plan to live here the rest of your life, you have no worries. If there's a chance you may have to move in 5 to 10 years, be careful (sounds like you'll be here a while).
Oh, is your city on the Cal aquaduct system? Some towns are not and in droughts suffer a lot (i.e. water rationing). If you're on the aquaduct, you will have to cut back during droughts, but it's not that bad.
Tankless water heating - try it first - find someone who has it and take a shower w/ it. It's often not "hot enough" - or that's the complaint I often hear. Running cables, coax, vacuum lines, etc. - the above posters are right. W/ a slab on grade house, you can't just go under the house in the crawlspace (there isn't one) and add these later. Some, however, can be added later in the attic. But since you have a two story, you're hosed downstairs. So yeah, install all those that you may want on construction.
Above all - mistrust your builder. When you ask him about red bolts and sheer walls, he'll grin condescendingly and say, "Well, you've sure been doing your homework, haven't you. Of course we use those. You really think we could pass inspection without them?" Or some such answer. If you want stronger than normal bolds, steel, ties and sheer, you may have to corner him. Then he'll act like you're asking for the Taj Mahal and try to charge you $8,000 that costs him an extra $1,200 and no extra labor. He'll get you somewhere. Be ready for that. Getting screwed somewhere is just a part of building a house. Just try not to get hosed too much. THat's the best you can hope for.
When you ask for extra stuff, try to figure out what these things cost. When you can say, "Gee, they're 99 cents each down at Home Despot, and you're charging me 50 times that" - it goes a long way. Note, it will cost - he does have to pay for labot - it does cost him more to step out of his "normal routine" and do something custom - but bargain. He'll always way, way overcharge. They can be pirates.
Oh oh oh. Floor creaking. Subfloor upstairs should be GLUED and/or SCREWED down to prevent creaking. Steps too. Trust me on this one.
If you're lucky you will have a "good" builder who will do a lot of this for you (w/out your needing to ask). But they're out there to make money, so don't count on it. Do everything you can. I'm sorry if this is all very complex, but if you can take care of these things, you will have a great house. Something will get missed - it always happens. Don't over-worry. Just do what you can and hope for the best.
Well, that's all I can think of. Sorry if what I say is off-putting, but it's stuff that might help you. Good luck!