Well to answer your question we need to know what you are going to use it for. A home defense gun will be differnat from a long range target gun. If you plan on shooting the CMP matches the gun is limited to a specific configeration. Now as far as mil spec why? mil spec means circa 1958 technoligy. gun steel, sights, and magazines have come a long way. The only thing that you need for parts compatibility is the pin size, and colt is the big one that screws things up there because they are the ones that made the differant pins (so the mil spec parts would not fit) however today there are adapters that turn a large pin colt into small pin so the other parts will fit. In my opinion (someone else will not agree with me) the Colt's are over hyped, over priced and not worth the money. The only reason I would buy a colt is if I switched jobs. For instance the police department that my buddy works at only allows offices to carry a colt AR15. Even while I was in Iraq the M4 that I shot baddies with was made by F.N., not Colt.
As far as the Smith and Wesson I have not used one but I have shot them and everyone I know who owns one is very happy with it. Now if you plan to put on alot of custom parts then price wise you might be better off to have one built or build it yourself. I always build my own because I have a standard that I cannot get from a standard factory gun. Again I must say that how you are going to use the gun is imporant here. As far a accuracy goes most quality factory guns will shot just fine for anything most people need. I know that my MK 12 will shoot better than I can, but I built it that way! Now most Ar15's lets say the S&W will shoot under 2MOA unless you get a lemon, so for most things thats fine. All of my AR15's and every one I have ever build will shoot under 1.5 MOA.
The really big advantage of building it yourself is that you can spread the cost around some. Matter of fact I still have parts that are waiting to be built into guns. (mainly because I don't need another AR now, but hey.) The big problem with home building is that if you don't know about the rifle the first build can fusrate you and all that. I know my first build drove me nuts, but I also learned alot and now I know what to look for on an AR I pick up. So no matte what you decide on that just keep that stuff in mind.
As far as the Ruger AR it is not a standard AR, several companies are making piston guns, and as you know the original is gas impingment not piston. Some people insist that the piston system is better (better how I always ask, because you can't get something for nothing.) The problem with piston guns is that first off if all other things are equal a piston gun will always weight more and be less accurate. Now the weight may be just a few ounces, and the accuracy differance may be very little but it is there. The reason is that the piston is attached to the barrel and changes the vibration and barrel harmonics. Since on an impingment gun nothing is moving on the barrel the accuracy will be better (remember all things being equal, piston guns can still be very, very accurate). Also you must remember that an AR with a piston I notice seems to cost more money.
People will tell you that the impingment system is dirty, and unreliable. well those people are just repeating stuff that they heard someone else say. One of my AR15's went 5000 rounds of wolf ammo with out cleaning and ZERO malfunctions. all I did was spray a few drops of CLP on the bolt before the range day and it never had a problem. I finnaly just got bored and cleaned it but it still never has a problem. My home defense gun went who knows how many rounds with malfunction and infrequent range cleaning. I finally broke some internal parts, but it was after about 8000 rounds on that gun. It got cleaned more since it is the home defense gun.
I would suspect that any quality factory AR will do the same if you use quality magazines and clean it every so often. With that I will close but I hope I have answered some of your questions. I think that a good investment for you would be to buy the gun digest "Book of the AR15" by Patrick Sweeney. You will learn alot, and it is a useful referance. I found his book after I had built several Ar's and had gone to the Middle East twice and I learned things I did not know. Reading his book will save you time, money, and ammo. Better to learn from the lessons of others right!
Now if you still have questions or things just send me a message and I will do my best to answer them for you.