One way is to alter population levels and citizen/freemen/slave ratios for all (or at least most) provinces. On other thing would be to increase the amount of cultures as the only provinces one get full manpower from is those with the same culture.
Or to do it more directly there is defines.txt where there are a few values regarding manpower gained (_CDEF_FREEMEN_TO_MANPOWER_ and _MDEF_MAX_MANPOWER_ are the values that you should look at).
Or you could add local_manpower_modifier = -0.5 (or some other value) for province_base_values in static_modifiers.txt (if doing that keep in mind that if doing that you may want to change the value for same_culture_group provided you want manpower to be gained from those provinces).
defines.txt is probably your best bet to do it quickly for all, but editing the individual provinces would be better if it is more important to just weaken the large nations.