When comparing PuTTY vs SSH of Windows' Linux subsystem, the Slant community recommends PuTTY for most people. In the question“What are the best SSH clients for Windows?” PuTTY is ranked 3rd while SSH of Windows' Linux subsystem is ranked 5th.
Ranked in these QuestionsQuestion Ranking
Pro De facto standard client for SSH, Telnet and Rlogin
PuTTY is one of the oldest and most popular clients. It has earned the trust of a great number of users over a long period by being reliable, offering useful features and helpful support. It got into the 15 Essential Open Source Tools for Windows Admins list by InfoWorld.
Pro Can be used on any Windows computer, even without admin rights
Pro Lightweight and portable
Doesn't require much resources (memory and hard-disk). Can even be run on a system by just downloading without install.
Pro Source code available
Full source available. Compile and modify it yourself.
Pro It's extremely easy to get running
All you have to do is go to the Microsoft store, choose a Linux distro you like, and install the client for free.
Pro Based on OpenSSH
OpenSSH is the reference for all ssh clients.
Pro Full Linux shell
Uses all relevant Linux ssh commands as normal.
Pro Excellent way for Windows users to learn Linux
It is much easier and more convenient than dealing with a dual boot Linux installation.
Con Can not save passwords
Anyway, you can use "PuTTYgen" to generate a key pair, then use "Pageant" to do a password-less SSH remote login.
Con Ugly design, too simple
Looks very dated. Does the basic functions very well, but not much more.
Con Lacks features
It is JUST an SSH client. There are many other options with built in X-servers, Multitabbing, etc.
Con only one session
cannot open a second session in the same window
Con Tedious logging/tracing
Its tedious to set up logging and tracing (e.g. for serial connections).
Con No global settings
If you want to change a setting for all your connections, you'd have to do it individually.
Con No login scripting
Con Graphical problems
For example running Midnight commander (MC) makes terminal blinking.
Con Crontab and other background jobs don't work properly
Crontab only runs on ROOT, and it needs Windows to stay open. If you close it, you will kill the crontab. Some background jobs don't run on Windows WSL.
Con Command line editing does not work properly
Overrides chars instead of inserting them... depending on position and moon phase?
Con Does not install on PC virtual machines
Con Forces window to a certain size
Any other SSH client will render the remote server at whatever size the local client window is. The built-in SSH client on Windows, however, forces you to use a standard size, and it's small enough to cause problems.
Con Windows' SSH key agent service is broken
Attempting to use the built-in ssh-agent provided with Windows will cause errors and authentication failures due to an incompatibility between Windows' ssh-agent and OpenSSH on remote systems.
Con Cut & paste works like the Windows prompt
Older versions of the Windows Command Prompt select text in a rectangular region of the console, rather than starting at a character position and selecting forward or backward along with the logical flow of text. To copy a sentence, for example, would require that you select all content in the two lines that contain the sentence, then trim what isn't needed, rather than just selecting the sentence. In later versions of Windows 10, this may not be an issue, as the cut-and-paste behavior has changed.