The 300 wsm is the most popular of the short mag series and I believe it has earned its place in useful cartridges but it is not the answer for everything. It equals the 300 win mag in performance with lighter bullets but because of the case length is not the best choice for bullets above 165 grains because of the bullet intrusion into the case thus limiting the amount of powder that it can hold also the short mags are intened to be used in short action rifles which makes for a lighter rifle to carry but also limits the seating depth of the bullet. I like the cartridge a lot and know several people that use them as their go to rifle and they have nothing but good things to say about them. I dont own one myself because I have a 7 mag that just seems to get everyting done although it is a little heavier and longer than 300 short mag would be.
What can said about the 30-06 that hasnt already been said? its a great cartridge my buddy Renny who shot the desert sheep featured on the website has a springfield 30-06 that he shoots round nose bullets out of and he has killed more game than anyone I know with that gun/caliber. if you are looking for more performance and want to keep it cheap you could have your 06 rechambered in the Ackley improved version which would only entail some minor chamber work, with that you would be able to get close to 300 win mag performance with the heavier bullets, I have another friend that shoots one of these and he swears by it but you would have to load your own ammo as it is not commercially available.
I guess what it comes down to is what you intend to use in your gun bullet wise and what you intend to hunt. For the lower 48 where for the most part we shoot non dangerous game the short mag with a 165 is going to shoot flatter and hit harder than the same bullet in the 06 (the 165 is fine for elk) theoreticaly the short mag would be lighter and shorter but that could negated by the action and barrel you choose. If I had more money and time I would have a 300 wsm in my quiver ( I already have an 06 and havent shot it in years because of my 7 mag)
I would have to say though, the only area that the 300 Win Mag shines above the 300 WSM is when using 200 grn bullets. The 300 WSM actually produces more velocity with 180 grn bullets than does the 300 Win Mag. It's a more efficient cartridge. The bullet seating depth has nothing to do with long or short actions. It is all about the style of your magazine or magazine well and how long the barrel throat is. This does not matter much because the standard seating depths are already producing superior velocities with both the 165 and 180 grn bullets with the benefit of better accuracy.
Anyway, if you are looking for an accurate 300 magnum, you can't do much beter than the 300 WSM.
You should base your cartridge on what quarry you plan on pursuing.
Short action guns with removable magazine can have more problems with bullet seating depth than nonremovable magazine because the removable magazine must fit the box on the action that holds the mag. This accompanied with a gun that has a long throat and you can end up being a challenge to get the bullet within a reasonable distance of the rifling. Most manufacturers in general use long throats for two reasons (and Weatherby is the worst), one is that it allows the shooter to pick and use whatever bullet they desire with out having to seat deep into the case and the other is that the long throats give higher velocities. More often than not the limiting factor for me is that the magazine is not long enough for me to seat the bullets out as far as I would like because the throats are so long therfore I end up with a bullet seated as far out as I can get it but it still is not as close to the rifling as I would like it. The answer would be for the manufacturers to ease up on the long throats and give us something that accomodates the median range of bullets available for a particular caliber rather that a one sioze fits all mentality