Best Practice for long term Linux/Ubuntu laptop usability

I have been using several Linux distros for about 20 years, and Linux as my main laptop OS for about 10. Several times, after installing software (notably different python or perl versions) or upgrading (apt-get upgrade) I run into incompatibility issues and instabilities which some times led me to reinstall the system afresh. I currently use Lubuntu (LTS version), and various Virtual Machines / Docker Containers to keep my critical applications running independently of my base system. Is there any *accepted best practice* about how to keep a properly functioning system for long term use, while having access to the latest version of installed software?