Basically there aren't many phone calls over non LTE based services. Especially since VoLTE can be used over WLAN via Wlan calling techniques. (the latter isn't supported in all networks.)
I think the problem is that with "analogue" each jump can use a hodgepodge of their own voip going from Analog -> Digital -> Analog. So you can get multiple, lossy compressions with varying settings multiplied together. With user-initiated voip, it's a single compression over the whole connection. So it could be better than user-initiated voip, or a lot worse.
At least that's my laymen's understanding of legacy phone systems.
VoLTE (Voice over LTE) have some other advantages over other calling applications. VoLTE is most likely on a very high QCI (priority), which means it probably has less delay and less packet loss than other traffic. VoLTE also often uses header compression over the air which means the packets gets a lot smaller and therefore also reduces packet loss. I don't think VoLTE usually have very high bitrate though, maybe around 10kbit/s. This is one area where other apps could be a lot better.
EDIT: I am of course only speaking about mobile calls. For landlines I agree that other applications provide better quality.