I believe, the problem is, various implementations of the same subsystems do not cooperate well (if they even cooperate at all). For example, NetworkManager does not cooperate with /etc/network/* or /etc/ppp/* or wpa_supplicant — it either steps away and does nothing or uses its own configuration (stored in completely separate manner). Sure, some approaches work (say, NM calls pppd, thus /etc/ppp/options have some effect), while some don't (good luck teaching NM to run PPPoE over 802.11 bridge).

This leads to a problem that one just can't have easily co-existing multiple approaches to work and configuration (i.e. "Ubuntu newbie" vs "seasoned GNU/Linux guru" ways). You have either one or another, and switching between is a pain.