As far as the Canon system is concerned, which is all that I have experience with, flash metering is no more intelligent than regular ambient light metering. If you point the flash at a predominantly pale/white object (wedding dress, white car etc.) the flash meter will still want to deliver you an 18% grey image so you will have to dial in some +ve FEC to keep your whites looking bright. That is one reason why you (should) have an FEC control. Equally, if you point the flash at a predominantly dark subject it will again attempt to render an 18% grey image, give or take. You need to use FEC to inform the flash that the subject you are aiming at is a dark object and not simply a poorly lit mid-toned object.
To further complicate things, if there is something lurking in the scene with exceptional reflectivity - glass in a picture frame, a window, a mirror, a white wall behind your subject - then the flash can be tricked into underexposing. The Canon flash metering system is generally very protective of highlights and if it sees a bright reflection coming back from the pre-flash it dials the flash right back, whether the reflection is from your "subject" or some other part of the scene. It is up to you to read the scene before you and set up the flash with FEC, just as you would EC for a picture without flash. Use of EC and FEC is quite independent but not mututally exclusive. You can use EC to adjust your ambient exposure up or down to taste and separately adjust your FEC to alter the flash. In this way you can make the background brighter or darker than your flash illuminated subject, as you see fit.
Another little quirk to be aware of, at least with Canon - if you point the flash head directly forward towards your subject (not tilted at all) the camera will use distance data from the focus of the lens within its calculations for the strength of flash required. In other words the distance data will limit the maximum flash output to somethig suitable for that distance, even if you have a black cat in a coal cellar. There is no point chucking out enough light to illuminate a subject at 20' if the measured distance to your subject is only 10'. This is great if you leave the flash bare. But as soon as you add some sort of diffuser/modifier (e.g. Omnibounce or Lightsphere) then they sap the flash of power. The flash does not know whether or not you have fitted a diffuser, so it bases its calculations on a bare flash. If you have a diffuser mounted then your flash output will be too weak. Of course, if you tilt the flash head in order to bounce then all bets on distance are off and the flash works purely on reflected light metering, which means a diffuser is fine.
Oh, and another thing with the Canon system - the Canon engineers have decided that at certain (lower) levels of ambient light, if you are using flash it must be your main light source and not simply a fill light. Well in the autoexposure modes the engineers have decided that it would be good to underexpose the ambient a little bit - up to 1 stop - and then allow the subject, illuminated by the (relatively strong, one presumes) flash, to "pop" out from the dimmer background. It also means that the additional light from the flash will not cause the background to become overexposed - if the background was metered at 0 EC and then you added flash, it would overexpose the background. This phenomenon is known as NEVEC and is documented here -
http://eosdoc.com/manuals/flash/NEVEC/. To be honest I'm guessing at the reasons Canon have programmed this behaviour in. It doesn't really make much sense to me to be fiddling about, secretly adjusting relative exposure levels without letting the photographer know - none of this is documented by Canon in the user manuals, or anywhere else for public consumption, as far as I know.
If you want real control over your picture then IMHO it is way better to shoot with manual exposure to control the ambient light and then let the flash do its thing, guided by your input through FEC. At least that limits the mystery to only one variable rather than two. For shooting indoors it is standard recommended practice to shoot in manual exposure mode. You choose the ambient exposure you want for the room conditions and then let the flash top off the lighting for your subject. By bouncing the flash you get to light the room anyway, to a point, but your ambient metering will not be hopping all over the place simply because you have a little bit more or a little bit less window or bare lighting in your frame. Also, by shooting manual you make sure you bring in enough ambient light to give the room a pleasingly lit look, thus avoiding the vacant black backgrounds and viciously bright faces that seem so popular with the point and shoot crowd.
Here's an example from my most recent wedding....
The camera was set in manual mode to generally capture the ambient light within the room, with flash used just to add some pop and top off the lighting for the subject. For this shot the camera was set to 800 ISO, f/5 (I needed the DOF), 1/50, 17mm. Flash was used, bounced off the ceiling and behind me to illuminate the B&G and the cake. You will also note that there is very bright daylight through the windows at the back of the room. Had I been using any sort of autoexposure mode I would have had a nightmare of a job keeping control, depending uponn how much of those bright windows was within my frame, as I moved round the room, shooting wide, shooting long etc. etc. Manual kept the room itself more or less correctly exposed (a little bit under, on purpose) with automatic flash, sometimes with a little FEC dialed in, completing my exposure. The thing is, the brighter I kept my ambient levels the less work the flash had to do, thus making FEC less of an issue as the flash only played a smallish part in the overall exposure. I'f I'd been on autoexposure and caught the light from a window in the frame I would have had hideous results. Much of the time, if I didn't need a large DOF, I was at f/2.8, which was fine on a short/wide zoom like the 17-55, and gave me an even better ambient exposure and/or allowed me to use a faster shutter speed.
Here's another example, again with manual exposure, this time at 800 ISO, f/2.8, 1/60, 200mm. The backlighting caused me no bother at all as manual exposure kept things where I needed them to be. Bounced flash (and a little PP of the raw file) helped complete the exposure for my subject.
By the way, I do not claim to be any sort of expert on all this. I'm still learning and it's early days for me in shooting in manual and also in the pressured environment of weddings. However, I know first hand the perils of combining flash and Av mode from the results from my first wedding, two years ago, which needed simply massive correction in PP due to horrible random exposures, but mostly severe underexposure. Hopefully, from the results in my sig link, you would not know how badly I screwed up that first wedding, but the shots SOOC were horrendous.
There are some examples of adjusting the balance of flash vs ambient here....
http://photography-on-the.net/forum/showthread.php?t=499526
and some words on the subject of using FEC from a guru on the whole subject of flash, here....
http://planetneil.com/tangents/flash-photography-techniques/8-flash-exposure-comp/
Have fun