Why not keep the list intact, but pre-select the country your visitor is in using geolocation?
Determine the user's physical location based on their IP address.
You can get started at http://www.ip2location.com/, but there are other free choices out there.
Do a Google search for city from "ip address", or country from "ip address".
Be aware that there are some physical divisions that are not apparent if you select a simple country. For example, the country France includes the French Caribbean, and if you are calculating port, you could be thrown off.
Apart from using geolocation, it is important to use the same list (and it is the same standardized list) used by Amazon, Google, Apple, etc. To see it, just go start ordering a product on Amazon and change your shipping address country.
The reason is that people who live in a given country are already used to selecting their country from this particular list, and know how to do it quickly. Any modifications that you make to the list, while well-meaning, will just slow them down.
Remember, people spend 99.99% of their time at other web sites. They know how to be efficient using the tools they've already come across. You should emulate those other sites whenever there is a standard way of doing things -- anything else will confuse your users.