Question: I have a lot of data previously analyzed without counting intronic reads. Should I reanalyze all my older data as well?
Answer: Using intronic reads has been shown to increase sensitivity (see here). If you would like to increase sensitivity and potentially capture cell types with overall lower transcriptome activity, rerunning Cell Ranger analysis with including introns may help.
However, if you are able to obtain biologically relevant interpretation from your existing data, you may not need to reanalyze your data with intronic reads counting.