You really need to feed us with specifics, ov3rhelming. That load order is very important with something so big as overhauls. Yet, what you says is known to me, I did witness it myself while using just FCOM but not at that extent you reports (at other thread I used this knowing to tell how a single gargoyle can mop the floor with a bunch of ogres thanks to it's high physical and magical defenses). Enjoying the opportunity for another shameless self advertisement

Afinity Sword may be the weapon that can help dealing with such monsters because it's magical damage bypass any kind of defenses albeit never being uberpower (albeit it can kill anything in a single hit, one should not rely it happening all the time).
But... the meaningful thing is... if the issue is not so generalized it's not a so bad issue, the critters that survive that epic battle will be dreadful enough for the PC.
In FCOM, Frans keeps things centered on the player, vanilla fashion. The foes will scale like the player in levels.
OOO is more place centered. This is the same as to says a low level char must avoid certain areas at all until enough leveled and with good equipment (someway more like Morrowind is). OOO will have some leveling too, but the extent is capped someway.
MMM and Oblivion warcry helps alot to increase the player's life insurance cost. This is specially true at lowers levels, sadly things begins to become frustratingly easy at level 20+. Indeed, before level 10 the player is advised to train speed as his most useful attribute and athletics and acrobat his better skillfriends.
Sorry for the long and boring post (but remember, Afinity sword may save your life without killing the fun and the dear danger sense) and will never allow it's own power reflected on you... Someone thought liches? (these guys are yet dreadful since they are specially addicted at damaging player's attributes and skills).