My feeling is that much of the confusion and frustration that gets labeled as "bug" or "broken" is because of "inferior design." Love my Reaper mind you.
1. Time timebase MIDI items. Pretty heavily discussed. Agreed upon by most/all as "bad." Exactly what has to happen to Reapers guts to fix it, I don't know. There's been several threads. Poofox's Bug Report and discussion thread is probably the hub of the matter.
2. Beats timebases themselves. This has received little technical attention. The definition in the help menu is incorrect. "Project elements will keep their position and length constant as measured in BEATS." No. It's determined by MEASURES and beats. This is why complaints arise about items getting shorter etc. Problem is not limited to MIDI items but it is very inconsistent with MIDI data contained within a single item. Simple example-
Everything was identical on either side of the Time Signature change before it was effected. Notice CCs in item versus (ReaControlMIDI) track envelope. There's other inconsistencies. Moving and copying things versus applying a time change among them. For example I could have cut the track in the pic, applied the time change, and pasted it back. It would have saved the item and envelope, but not the marker positions.
Of course, there is other complications. Like, "Remove contents of time selection" and "Insert empty space at time selection" could cause very odd fractions of beats to be introduced. But that seems like a detail, not the root of the problem. I also don't mean to say that what I write here covers everything.