Annotation format design
Presuming we consider "human readable", "easily parsable", and "quickly queryable" to be objectively good qualities (and if not, I worry for the future):


Text-based: It's absurdly common to want to use grep or awk on annotations. Sure, one could make variants of these that are binary-format aware, but why reinvent the wheel. Of course text files don't innately allow region-based queries of their contents, so on to point 2...


This should further explicitly be line-based. Fields would need to be tab-separated (ideally it'd use the ascii record separator character instead, but I fear that ship has long ago sailed).

A strictly defined line order: This is one of my personal pet-peeves about BED/GFF/GTF files. If you're going to make a text-based annotation format, everyone would end up ahead if said format made explicit that it should be sorted. This then allows things like tabix to be used so the "query a region" problem is then solved. But I would go further than that. The issue with things like GFF is that there are multiple inter-dependent lines and there's no strict rule about whether a parent line absolutely must come before a child line. This just makes implementing things a nightmare and more often than not a randomly ordered file will just break tools. Since GTF or GFF-style interdependent lines likely be how any annotation format works, this ordering between lines with the same start position should be made explicit in the format.