The otehr thing is that miniatures and models and such are actual physical objects that properly show light in the environment.
The ideal, to me, would be a mix of physical objects being shot for as much as possible, and resorting to CGI only for those shots where you CAN'T do what you want to do. Example: one of the main actors is playing a part that requires latex mask work. The mask, however, can't undulate (even with bellows) quite the way you want it to. So, you shoot the actor in the mask, and CG in the undulation. (Isn't this what they did for Davey Jones in Pirates 2?)
Example 2: You want a giant mountain ogre to attack your heroes. You create a physical prop a la the Rancor, and shoot it doing as many things as possible, then CG transitions and perhaps some movement for the more "exposed" shots. Do it well enough, and people won't be able to tell which is the physical object and which is CG.
To me, CG should be used to "cheat" the camera. Transition shots, impossible stunts, cleanup work, etc. To this day, I maintain that Jurassic Park is THE benchmark for CG work. It is (at least as I recall) a seamless blend of animatronics and FANTASTIC CG work. Now, admittedly, it's been YEARS since I saw the film, but I recall it being basically indistinguishable as to which was a physical object, and which was the real thing. I only found out years later that they used animatronics in the making of that film, and CGed other shots. To me, that's the best way to go.
Your actors have something to play off other than a tennis ball on a stick. Your crew has something to light. Your CG team now has a physical object that they can meticulously copy, too, instead of trying to make a dinosaur out of nothing.
Oh, and you got that DEAD ON accurate re: the Transformers CG models. They just look like blobs of metal to me. That may be the idea, but it's not at ALL interesting to look at for me, and I found it detracted from my enjoyment of the film. Well, that plus all the Michael Bayisms and Baysplosions. But I digress.
The ROTS scenes also seemed jumbled, but I think that has more to do with how they were framed (because they could use CG), how fast that sequence happens, and the fact that I mostly didn't give a crap. By contrast, the shots of a similarly frenetic space battle in Serenity were (to me) awesome at the time, and I still thoroughly enjoy the shots of the space battle in ROTJ. And, of course, the surface attack and trench run in ANH are top-flight. So, while some of it is the business of the shots, I think a lot of it is also how shots are framed BECAUSE you could "do more" with CG than with models.