This should be some that is doable for your work. One tool that will be helpful in scripting is the Feature Compare tool which will compare a number of variables. Using this tool we should be able to script this for all of your layers. This could also be done through ModelBuilder.
Feature Compare:
ArcGIS Help (10.2, 10.2.1, and 10.2.2)
This is a sample workflow logic that could be used to script this process:
import arcpy, os
#Create DB Connections to both databases
gdb91 = r"DB Connection"
gdb101 = r"DB Connection"
#Create a list to store the feature classes from both databases
list91 = []
list101 = []
#List the feature classes
arcpy.env.workspace=gdb91
fcList = arcpy.ListFeatureClasses()
for fc in fcList:
list91.append(fc)
arcpy.env.workspace=gdb101
fcList = arcpy.ListFeatureClasses()
for fc in fcList:
list101.append(fc)
#Compare the feature name and them compare the feature classes themselves
for fc91 in list91:
try:
idx = list101.index(fc91)
fc101 = list101[idx]
path91 = os.path.join(gdb91,fc91)
path101 = os.path.join(gdb101,fc101)
arcpy.FeatureCompare_management(path91, path101, out_compare_file=r"C:\CompareFile\{0}.txt".format(fc91))
except:
print "Cannot compare layer {0}".format(fc91)
