There certainly are a lot of thoughts about archaeopteryx, however I would not, as an evolutionist, cling to tightly to that transitional form. Was it cold-blooded, warm-blooded - there's a lot of debate on exactly what it was as I understand it. From what I've read I think it was a bird.
I just look at the duck-billed platypus and wonder what people may have thought of that if it was dug up as a very old fossil.
We'd likely have 350+ peer-reviewed books written by very well respected scientists about a new path of evolution involving birds and mammals.
As far as microevolution - nobody (sane) disputes that - but microevolution and macroevolution are not at all the same thing. Microevolution typically describes things that are already predisposed in the genetic code. Microevolution is how you can breed small and large horses in a very short aount of time, or how you can see changes in fruit flies in a short amount of time, or Darwin's finches... It does not explain or have anything to do with how a lizard grew wings and became a bird. Again, is it punctuated or gradual? Or both, perhaps?
Some things are not easily explained by gradual change over time. That's why punctuated equilibrium is so popular - it bypasses this problem (though for some reason, depending upon the discussion angle, gradual change and natural selection are still brought up when it is convenient). But then you have to deal with the math again - how many beneficial mutations ("hopeful monsters" as I've heard them called) do you need to happen to get where we are in about 1-2 billion years' time?
Most mutations (and I do mean most) are not beneficial (several examples have already been given in this thread of diseases, harmful bacterium, cancer... none of which are beneficial.) And if one beneficial mutation manages to make it through and gets eaten by a predator? Well, we need to start over and wait another 10,000 years... or 1 million years for a big comet, I dunno.