awk -F, '
FNR == 1        {FCNT++                                                                                         # inc file counter with every new file
                }
FNR > 1         {KEYS[$1]                                                                                       # keep $1 in an array; overwrite duplicates
                 for (i=2; i<=NF; i++) W[$1,FCNT,i] = $i                                                        # keep fields in array indexed by key, file No., field No.
                }
END             {printf "Key, diff columns"                                                                     # start printing header
                 for (i=1; i<NF; i++) printf ",f1_value%d,f2_value%d,value%d_diff", i, i, i                     # complete header line for all fields
                 printf RS
                 for (k in KEYS)        {for (i=NF; i>1; i--)   {N1 = W[k,1,i]                                  # for all keys, for all fields, get values
                                                                 N2 = W[k,2,i]                                  # for both files,
                                                                 D1 = N2 - N1                                   # and calc difference
                                                                 OUT = sprintf (",%s,%s,%s", N1, N2, D1) OUT    # collect all those in temp var OUT
                                                                 if (D1) COLS = ",Value" i-1 COLS               # if diff exist, collect fields in temp var COLS
                                                                }
                                         print k, "\"" substr (COLS,2) "\"", substr (OUT, 2)                    # print all those, cutting off leading comma
                                         OUT = COLS = ""                                                        # reset temp vars
                                        }
                }
' file[12]                                                                                                      # OFS and SUBSEP relict from development, not needed