Fox, I've had both in the past. I recently sold the last 35 Whelan I had. I have kept three 338-06 rifles though. Two built on Winchester Mod 70 actions and one on a Ruger #1.
The 9.3x62 isn't a bad cartridge by any means but it's usefulness is a bit limited IMHO. Not because it isn't capable of clean kills or accuracy out to 400+meters. Bullets are very difficult to come by if you hand load is mostly the reason.
I stayed with the 338-06 mostly because of the great bullet selection, the rifles I have are very accurate/predictable/dependable. I also have a 338-08 which is almost as effective.
Just remember, the heavier the bullets at decent velocities the heavier the recoil.
The one drawback of the 338-06 is that cases nor loaded cartridges are available. The 35 Whelan can be purchased off well stocked LGS shelves. I checked out several different gun shops last summer and only one, Del Selin's in Vernon BC, carried loaded ammo. two others carried 35 Whelan brass and only three carried 35 cal bullets suitable for the cartridge.
Not a big deal because all of the above utilize the 30-06 case as a parent. All are easily necked up and fire formed.
Ballistics comparisons show very little REAL difference between all of them.
SOCIALISM THRIVES ON POVERTY
TURF THE LIBERALS IN 2019
Liberals really like POOR people, they're making more of them every day
If you can't vote CPC, stay at home in protest