The 338-06 wasn't one of the OP's choices and neither was the 9.3x62.
Didn't anyone read post #1?
I don't know, seems like a pretty honest mistake to make, given that the 338-06 and 35 Whelan would be more of a head-to-head comparison, really isn't much of a comparison of 338 Win Mag to a 35 Whelen? More likely comparison to a 338 Win Mag would be a 358 Norma Mag.
Must be nice to be perfect and never make a mistake... some day you'll make a fine wife for somebody....
Now back to the OP's actual question of 338 Win Mag vs. 35 Whelen, it would pretty much come down to the user's level of recoil tolerance.
Some advantages to the Whelen are: larger magazine capacity (in a bolt action) without the need for a drop magazine; able to use 38/357 pistol bullets for reduced/small game loads; available in larger range of action type, IE. pump.
IF one
was to entertain the thought of a 338-06 vs. the Whelen, the best choice would then most likely be a 338-06: better bullet selection, better penetration, better wind bucking/trajectory, etc. There is a reason that Elmer Keith eventually decided on a 33 over a 35. On the other hand, if one wanted more horsepower out of the same cartridge head size, the obvious choice would be a 9.3x62. Of the 3 (338-06/35 Whelen/9.3x62), the ones on either side of the 35 Whelen do a better job.
I've always been kinda underwhelmed by the 338 Win Mag. Owned one for a while and came to the realization that it didn't do anything one of my 300 magnums wouldn't do with a stout 200 grain bullet. Then I bought a 340 Weatherby and found the ideal cartridge case for the 338 bore.
The 358 Norma would possibly be a better choice than the 338 as well, but we better be careful or the Post Police will come around and scold somebody for mentioning some cartridge that wasn't mentioned by the OP.
Although nowhere as near as popular, I'd put the 9.3x62 ahead the 338 Win Mag too. Very similar ballistics with 250 grain bullets, better selection of heavies, five down instead of 3.
Personally, the only 35 Whelen I'd consider is a Remington 7600, just 'cause.