This somewhat depends on your analysis. QIIME 2 is a full pipeline: clustering/denoising and annotation, tree building, diversity calculation and visualization and several statistical tests. The plug in system means that are are more and more tools being added - useful for bringing in new techniques.
Personally, I tend to use QIIME for about 80+% of what I do, with a mix of command line and python API. I occasionally use the underlying tools because I want control of a specific aspect of the analysis that I find harder to access through the QIIME APIs.
The other place I think many people chose not to use QIIME is for plotting. Emperor works well for me, but sometimes it’s easier to adjust plots on my own in the underlying or other software than to use the ones directly from QIIME and try to adjust label, colors and fonts. Unfortunately, what looks good on my screen often isn’t readable when I go to a figure panel. So, this might be a place where you’d want to go to ggplot, or prism, or seaborn, or excel… or whatever else your favorite plotting library is, and use that.