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?
Why not both? It's still evolution. And why don't regulatory genes -- genes controlling the expression of banks of other genes -- 'explain' how a lizard grew wings? After all, the ancient homeobox genes appear to have proved malleable enough to generate body plans for both insects and vertebrates , despite how different *those* look. There is , of course, a large literature on bird evolution, evolution of flight, evolution of limbs....care to actually delve into it, or are you content to merely pose questions as if that proved science had no answers?
Some things are not easily explained by gradual change over time.
Primarly, the 'sudden' appearence in strata of numerous new species. But as the granularity of the fossil record increased, the meaning of 'sudden' changes. We tend to find more 'ancestors' the more we look...so those 'sudden' appearances aren't so. And of course, in geologic terms 'sudden' is still a vast amount of time...beyond what most people can grasp.
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?
Evolution rests on four facts of life: variation, inheritability, selection, and adaptation. It's not just about mutations (variation). And there aren't just 'beneficial' and 'deleterious' mutations: there is also a large class of 'neutral' mutations which affect gene frequencies as well.
You seem to have quaffed the ID/creaiotnist kool-aid -- have you at least *sipped* the scientific rebuttal to their tediously repeated 'problems' with evolution? It's not like these issues haven't ever been addressed.
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.
Then again, some mutations are beneficial in some contexts, harmful in others....sickle cell mutation being an example. A simple understanding of biology will only get you simple answers.