this is an interesting thread and i will attach some more information to it.  (i own neither a 35 whelen OR 9.3x62 ...yet 
this is a list of cartridges and their water capacities in grains taken from 2 sources:
30-06   69 gr
35 whelen   70/71 gr
338 winchester  85/86 gr
9.3x62    77gr
9.3x74r   82gr
375 h&h   95gr
so, clearly the 9.3 has an advantage in case capacity.  also as bore diameter is increased, the same weight of projectile, at the pressure...the larger the bore, the faster the larger/more energy the larger bullet will go with the same power plant.  there are efficiency gains, take for instance the
7mm mag:  3000 ft lb    175 gr
338 win :     4000 ft lb    250 gr
458 win:      5000 ft lb    500 gr
3006-          3000 ft lb    180gr
35 whelen   3500 ft lb    250gr
of course this is a generalization.  it would 
appear that a 35 whelen with less case capacity AND bore diameter, pushed to the 
SAME pressures would have slightly less energy with the same weight bullet.
now 
@Bob Nelson 35Whelen this is not me dirt shirting your favorite caliber, this is just an observation based on previous information i have seen/read  i will follow this up with an article from a site called impact Dynamics