1. VIB Author is a command line tool for Linux (distributed as rpm package) - ESXi5-CPT runs on Windows. If you are developing ESXi device drivers or other binaries on your own then you will do this in Linux anyway (and might even do not have access to a Windows system), so VIB Author might be the better choice then. However, if you just want to build a VIB package for a persistent firewall rule or a package containing pre-compiled Linux binaries then you do not necessarily need a Linux system, and might prefer ESXi-CPT to do the job on your familiar Windows box.
2. ESXi5-CPT is GUI driven and just needs the payload file in tgz (= tar.gz) format as input. It will create the descriptor file for you after presenting a GUI for defining the values for the required XML tags (for some of them defaults are provided depending on whether you want to create a firewall rule or a hardware driver package). In contrast VIB Author is a pure command line tool that requires the descriptor file to be created by yourself (though a template is provided as part of the tool). For creating the payload file it expects a build directory that contains all directories and files that should be part of it (A good idea - I guess I will steal that for the next release of ESXi5-CPT ;-).
3. Both VIB Author and ESXi5-CPT allow you to create VIB files with an acceptance level of CommunitySupported only. This is not really a limitation of the tools, but due to the way how VMware certifies software and offers support for it. VIB Author can optionally add an electronic signature to the VIB file, although this is not required for CommunitySupported packages.
I strongly recommend reading the manual of the VIB Author tool, even if you are not going to use it, because it offers some interesting background information on building VIB files (e.g. what directories you are allowed to add or modify with a CommunitySupported VIB package - yes, this is limited!). But I also recommend reading the project page and manual of the ESXi5 Community Packaging Tools to be able to compare both.