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I believe that mate with King, Bishop and Knight vs lone King can take up
to 49 moves, which is the reason for the 50-move rule. IIRC, computer
studies of more complex positions have shown  mates requiring over 200
moves--which might or might not transgress the fifty move rule, as any
capture or pawn move resets the clock.  But in any case, the line has to
be drawn somewhere and some wins (if arbitrary length games are allowed)
will be draws under an x-move rule.

I believe the 50-move limit should be increased for a larger board, but
reduced for more powerful pieces (for the board size).  The technical way
would be to calculate the average crowded board mobitity of each piece
(using Betza's method), then add up these values to get an approximation
of the power on the board. Compare the ratio of this power to the number
of squares to the ratio of the FIDE army (about 64, depending on the magic
number) to 64 squares = about 1.  

The formula is movelimit = 50 times board size divided by total army
mobility.  For FIDE Chess this is 50 * 64 / 64 = 50.

To examples for your duodecimal game:

1. Total army mobility = 90   50 * 144 / 90 = 80
2. Total army mobility = 200  50 * 144 / 200 = 36

You can probably guesstimate accurately enough without actually doing the
calculations.