It has been a long, long time since I played stock SH3. Part of me says you should do it just to know how much work went into the mods.
The mods totally change the game. One of my favorites is the simple mod "Torpdeo Damage Final 2" so you can actually see damage when you torpedo a ship.
GWX totally changes the game. Aircraft are merely a nuisance otherwise. They are at best mission-enders in GWX. At worst they are career-enders.
There is more variety in ships.
I highly recommend GWX.
Also SH3 Commander.
Steve