From: Basement of the Alamo
If just beginning, I would probably recommend SC2 The War in Europe. That way you can leave off learning the Pacific Theater for another time.
The big strategic difference between the two is the scale of the maps. SC2 WIE, with its focus solely on the European Theater, gives you more hexes to play with and consequently more room to maneuver. And obviously none of the participants have to devote much time to what Japan and China are doing or not doing, although you will get the occasional newsflash. You also have less naval battles to manage. In addition, you don't have to witness Italy's colony in in the Horn of Africa slowly getting strangled. WiE also has the advantage of longer and deeper development although I'm sure WaW is constantly being updated.
When saying which is best, it really comes down to preference, Some players prefer a global battlefield. Some just prefer a European theme.
"They couldn't hit an elephant at this dist ...." Union General John Sedgwick, 1864