Yes, the LEGO rocks don't look PERFECTLY like stone, but it's a toy. It's not SUPPOSED to be perfect. And if a rock looks exactly like a rock, you can't use it in innovative ways. Some time ago I saw a number of interesting models that used parts of the round rock parts as engines in spaceships and steampunk airships. Thus, I am of the opinion that any type of part which can only be used in one way should not be made at all (And yes, LEGO has produced such parts in some sets, but for the most part they don't have this problem).
LEGO has also made some printed baseplates and raised baseplates and such (http://www.bricklink.com/catalogItem.asp?P=2359px1 , http://www.bricklink.com/catalogItem.asp?P=3947bpx1 , etc). And LEGO also (In most cases) puts studs in most areas except printed areas (such as on roadplates), meaning that there is no restriction at all on where you can put stuff. If you want an area with no studs on it, there is a simple, novel solution: Put tiles on them. Covers up all the studs, but doesn't permanently remove them. And I would consider the lack of studs to be bad in terms of trying to connect figures. Minifigs don't tend to balance well with no studs underneath them.
In terms of minifigures, I do agree that MB does have SLIGHTLY (less than 1%) better minfigures because of the ball joint design allowing for more positions. However, MB minifigures have a major disadvantage that their figures are so detailed that it looks funny if you try to make your own figures because the printing and such doesn't match well (Which LEGO has had some minor problems with recently now that they are printing the legs, but not to nearly the extent that MB does). As I said before, anything which imposes any limitations (On purpose or not by the company) is inherently bad for creating new things.
Yes, you are completely correct on this point: Megabloks is much better at making large structures easily than LEGO. For example: http://www.my-family-fun.com/pictures/mega-bloks-pirates-of-the-caribbean-port-royal-275.jpg. Notice that the entire bottom section is made of one part (I think). This means that kids don't have to (Or as I see it, don't have the option to) brickbuild it. Another example of an overjuniorized part that could be made out of several smaller parts except that they care more about the money they get for their low quality sets than improving the quality. And yes, they do kill on looks (By kill I mean the buyers might die from the shock of buying such a crappy looking set rather than someone paying THEM to take it, more on this in the next point). I would not call LEGO's advantage in quality and clutch control "Slight". A few months ago a friend of mine got a Megabloks set (An old Pyrates set I think) and I borrowed a few parts to check the quality compared to that of LEGO. I noticed that 3 of the 8 parts I grabbed were supposed to be the same color (According to this friend at least), and yet the colors were very different. The parts were supposed to be orange, one was slightly yellowish, one was brown, and the other one was mostly orange, but had streaks of a greenish brown color running through it (No pictures, didn't have a camera with me, sorry). I then decided to try and put the parts together to check the clutch power. Most of them wouldn't even go together, or would go together and got stuck. I also noticed while trying to put some of them together that they bent quite a lot when I squeezed them. This shows that the color consistency and clutch power are both FAR below that of LEGO.
I'm not sure what you mean by "outdated standards". The only "outdated standard" (from Megablok's point of view at least) is an adherence to high quality control. LEGO made products free of lead and mercury and all the other dangerous chemicals years before they were required to, they purposely make sure there is little to no risk of being cut or anything by LEGO (which I have heard from some people of having happened from Megabloks and other competing brands), they continually make sure that there is high color consistency and clutch power. They also often fix problems they find with parts (Such as fixing a problem earlier this year with their ball-joints cracking apart). LEGO has also experimented before (Both with making new types of themes, such as StarWars and other licensed themes, and in making new parts, or in moving into other types of toys (such as electronics with their motorized parts and robotics sets)).