Actually, if you look at the probability (statistics), for each level of complexity, the probability of evolution decreases. That is because when you have two percentages, you have to multiply them. So, if you have two items, yes, a correct mutation for both would be a boondoggle for evolution, however, the probability of this happening goes down significantly. It approaches statistical impossibility (10 to the -50th). And each mutation that occurs is another level of statistics. Another set of percentages to multiply, and in just two generations, you have already well surpassed statistical impossibility. And, this is supposed to have gone on for billions of years.
As gluadys has pointed out, you should not simply be multiplying the probabilities, at least if you want to calculate anything interesting. Consider that, by your logic, it would also be impossible for me to be here. I have roughly 100 new mutations (compared to my parents). The probability of my getting exactly those 100 mutations, out of the 6 billion bases that could have mutated, is staggeringly small (something less than 10^-700, I believe). In other words, the probability of getting to
any particular genome by mutation is extremely small. Since these low-probability events actually happen all the time, the fact that a particular set of mutations is improbable doesn't tell you anything about whether it has happened.
A better way of looking at the question is to consider the probability that a species will change, rather than whether it will change into something specific. After all, evolutionary theory does not propose that fish were attempting to evolve into air-breathing land animals. What it proposes is that fish kept changing, and that some of those changes were beneficial, and that some of those beneficial changes happened to involve the gradual development of limbs and lungs.
The probability of change happening to a species is high. For a reasonably sized population, every gene in the genome will experience something like four mutations each and every generation. If there are any beneficial changes possible, they are quite likely to be hit upon by mutation.
The fact is, the rate of long-term morphological change in the fossil record is many orders of magnitude smaller than the observed rate caused by natural selection under changing environmental conditions. To the extent that we can tell, evolution by mutation and natural selection is entirely plausible.
One thing with genotype is that it takes significant changes in genotype to affect phenotype, since the typical gene is 1000 nucleotides long. We're not talking about slight changes in color or protein function. We're talking about turning a fish into a land-breathing animal.
Actually, turning a fish into a land animal is indeed largely a matter of slight changes in protein function and timing. The basic cellular machinery and the body plan is the same for both, and most organs are quite similar.
That would require billions and billions of mutations to occur on top of each other in just the right way to not kill the creature.
Where on earth did you get that number? That would mean that there have been ~250,000 changes in every gene in the genome, which is ridiculous. Even if you include regulatory regions, you're requiring every base in every gene to have changed 50 times over.