This is one of those things where the reality and desired course of action are divergent and data service providers seem to need to choose between what people think they want versus the complex realities of science. Are life scientists the proper audience to "democratically" decide what "primary" means?
In my opinion, the term "primary" leads people to believe that a subset of the transcripts is more important than the others - they will study these more, hence becoming a self-fulfilling prophecy of 'importance'. It sets back science rather than promoting it.
I can't see the benefit of a new terminology for things that are already defined. Clinically relevant, longest exons, high abundance, low abundance we all know what these words mean. Whatever temporary benefit of a seemingly consistent naming pattern might be, the information will start changing the next day. And now we have to deal with those changes via a new and potentially misleading term. Why not just call one set "clinically relevant (as of 2018)", the other "high abundance" etc and let people filter by those.
The real challenges are in matching/summarizing one data release versus the other (or across versions), finding out what the differences are in between, visualizing them easily.
What we really need are accurate transcripts, ways to annotate or filter transcripts based on observed abundances in tissues or conditions. What we need is information that helps cut down on the busy patchwork of "custom" little scripts to figure out simple information.