- Which faction is stronger? (Necropolis, Tower, or Conflux)

The downsides of Conflux: dependence on a large number of resources, vulnerability to certain magic, weakness of some units (fire mages and earth elementals)...
In a confrontation, the undead will most likely be in first place...

I agree that Conflux has relatively weak units at levels 4-5, but this is balanced out by the first and last units... Plus, the use of Armageddons :)
And it will be very difficult for necromancers, at least because there are no living creatures in Conflux.