tiny-count is a very versatile tool, with the proper feature selection configurations, it can be adapted for isomiRs, nucleotide editing and so forth.
What I would love to see is a set of example configurations that can cover more types of transcripts. Think of the endogenous alignment priorities offered by exceRpt, but more elegant (and maintained in the current decade).
Having this kind of example config in the repository (based on dashr, or a similarly comprehensive annotation dataset) would be great.