Another thing that must be considered anytime a criticism is leveled against the fossil record is that paleontology is a very recent science. It is only 100 years old, and so is really only in its infancy compared to other sciences. One reason that there are gaps in the fossil record is that we haven’t been looking that long! Most of the discoveries that link dinosaurs to birds have only been made within the last five to ten years. One of the most famous dinosaurs, Velociraptor, was only discovered weeks before Jurrasic Park began filming. Given the luck associated with fossil hunting, the huge variety of potential species, and the time needed to study them once found, it could potentially take hundreds of years before enough of a fossil record is put together to even begin to answer all the questions scientists have. Even then, due to the random nature of fossilization, we of course should expect gaps.
I also wanted to address a common misconception about evolution. Some people say things like, "Well, if amphibians evolved from fish, and are therefore superior, why are fish still around? Why are any more primitive forms around for that matter? The answer is easy. Natural selection generally occurs in response to a local condition. The most famous example is the micro-evolutionary example of butterflies in England during the mid-1800s. A certain species of butterfly lived throughout England. They were generally white, a color which camoflaged them against the bark of birch trees so they would not be eaten by birds. From time to time, however, a black butterfly would be born (a mutation, not unsimilar to the variations in eye color or hair color that humans experience). The black butterflies would sadly try to hide against the birch trees, and immediately get picked out by the birds and eaten. The mutation would still occasionally occur, but the black butterflies generally did not survive long. Eventually, the Industrial Revolution came along. Massive coal burning factories pumped unfiltered coal dust and smoke into the surrounding countryside, and the formerly pristine birch forests turned black with soot. Suddenly, the white butterflies lost their camoflage advantage. The few black butterflies began to survive, and the white ones began to die off rapidly. With almost no white butterflies left, the black ones bred with each other and began spreading the black color gene. Thus, a local environmental condition “naturally selected” them for survival. A new subspecies was created. Note that this in no way made the white butterflies go extinct! They continued to survive in other areas of England without pollution. Likewise, a new species might develop in the natural world in one area, but remain perfectly adapted in another.