actually, A or S (if you use Canon), functions are great depending on the situation.
When I shoot sports-related photographs, I use shutter priority a lot, just because there are certain shots I want to capture still and some shots I dont, and on manual mode, it will make me "miss" the shot I want if I keep adjusting for the shutter/aperture. So, I wouldnt say dont use A or S mode, but you need to know what you're shooting.
Also, if you go in and out of a building a lot when you shoot (i.e. on sight seeing vacation), it is good to set on Aperture priority mode, which I use fairly often just for general purpose, and I dont hve to do too much and adjust all the time.
When I shoot something that I know that I will do some processing or just want to get "the" shot, then I use M then adjust it from there.
On the ISO, rule of thumb for me is if I am shooting interior, I use ISO400 at most or sometimes 800, depending on the importance of the photo I guess.
Shooting outside, I always stay at 100 or 200 at most.
I have pretty fast lens, so I can afford to stay at 400 or under doing interior shoot as I have a 17-55 f2.8 for general purpose lens and also 50mm f1.4 and 70-200 f2.8 IS.
So, good lens can help you a lot in terms of the setting flexibility.
PS. The above knowledget are EXCELLENT!! Those are perfect for those who just begin in photography and those are all you need to know when you start out. You dont need anything else.
once you master all those, then you can start thinking above of the TTL lighting/exposure/metering algorithms and etc to think about the photo.
Personally, I use ETTL mostly on my flash and I find canon camera body + speedlight 580EX II do very good job in calculating what I need. (plus I'm lazy shooting in Multi/M or TTL modes most of the time anyway).