I have been experimenting with manual and aperture priority over the past few days. My basic config is to use a higher f-stop, set ISO at 100 to 400 with flash. I started with f-stops in the 9-12 range. If the camera selects a slow shutter that can't be hand held, I am over riding to a hand held value to get more keepers. If the camera allows, I am using a single focus point so I can place the focus where I want. (Typically the eye closest to the lens.) I have been pleasantly surprised at the results. My prior depth of field issues have been resolved. I noticed that program on most cameras will try to use the minimum f-stop of the lens even with flash. Some of my go to lens are f1.8, f2.0 and lots of f2.8. F1.8 has almost no depth of field. So on automatic I might get the eye in focus, but the tip of the nose and ears are out of focus. Running up the f-stop helps quite a bit. F 9-12 is probably overkill, but it is having the desired effect. I am going to try and dial down the flash out put next to try and soften up the effects of the flash. Has anyone else here tried the higher f-stops with your doll photography?
I don't know what you're using for light but I'm routinely shooting at 5.6 - 8. I'd be very careful about using flash. On camera flash doesn't flatter people or dolls either. If you have harsh contrasty main light then some fill flash makes sense or off camera diffuse flash makes sense. Personally I prefer putting the camera on a tripod rather than breaking out a flash. Also, unless you're using a very old camera you can probably safely run your ISO up to 800 or even 1600.
It's all really personal preference, I think. I shoot just about everything in 1.8, because I want that shallow depth of field to add realism to tiny people in a big world, but in order to control the other variables there it's best to shoot in manual and manually focus. (I tend to zoom in on the eye after framing a shot and make absolutely sure in magnification that the lower eyelashes are in focus.) I use natural light and try to keep my ISO low, but in the winter I'm more likely to crank it up to 400-800 to accomodate whatever ambient light is around than use flash--I'm sure someone out there can use it to their advantage, but I feel like it flattens everything out. The 1.8 helps there too, because it's a wide open aperture that takes in more light in general than my kit lens.
I am with everyone else. It is a matter of what you are after. Also, what you are shooting and from where. If you have a large doll, shot from a fair distance and what you want is background blur and bokeh, you need a lens that will open up to f/1.8 or larger. If you have a small doll, shot close up and want it all crisp and detailed. you need to go to f/22. So, the aperture you use depends on what you are doing. I am with TomB, that the vast majority of home studio shots (which tend to be taken with table lamps, let's be honest) need a tripod. This is particularly the case if you want sharp-throughout shots. This is because smaller apertures need slower shutter speeds (you knew that). You can also raise the ISO. Find out how high your particular camera can comfortably go in ISO. If it is a popular one, someone might already have checked it out. If not, do some sample, low light shots and compare. ISO100 shouldn't be needed unless you want to print at billboard size or have a ropey camera. Most modern DSLRs can cope very well with ISO400 (which is my default) or above. Then set your aperture, according to how deep a depth of field you need. So, it varies shot by shot and you have to make calculated decisions about what you want to achieve and what is the best way to achieve that, given the technology.