Shortcomings of automated analysis tools
As you have probably gleaned by now, automated analysis tools are excellent for the initial analysis of a malicious sample and can provide a wealth of information in a brief period of time.
However, these automated analysis tools are not without their shortcomings. First, they are often reliant on signatures and heuristics to detect malicious activity and cannot apply the knowledge of a seasoned malware analyst to a sample. Put simply, they are still machines and their classifications are not always correct. They also may not be able to react to certain sample conditions, such as the usage of analysis evasion techniques, or packed samples.
Some shortcomings of public tools are addressed by private, own-infrastructure sandboxing utilities such as Cuckoo, but these often introduce other problems, such as infrastructure to run the sandboxing framework and the cost of people maintaining it.
It's important to keep in mind that while...