wikenigma I think you made the right choice with a custom template.
The way I generally see it, if you want to customize the look and/or location of things, then a template is what you want to do. If you want to add features, then a plugin.
So far my dev experience with DokuWiki indicates that I need to focus on the latest release of DokuWiki Core. If it receives an update, then I need to test it. The rest is extra depending on your template. Like if you want to customize the look of say plugin:discussion, then of course with each DokuWiki Core, you'll have to update plugin:discussion.
Been using DokuWiki for several years now. Once I understood what is permanent and what's not, I never had issues upgrading.