The World Tree model is the only time the Realms have had a unique cosmology that was specifically designed with the setting in mind. As barebones as the model is, I find it the most natural fit for the world of Toril.
Yes, as others have pointed out upthread, Greenwood originally used the Great Wheel when he adapted the world of his stories for D&D. However, I don't have the impression that Greenwood ever considered alignment a major part of his world. For example, the edition-neutral Elminster's Forgotten Realms (2012), which presents a vision of the Realms more close to his home games than other WotC or TSR material, spends precious little time on alignment. Even the writeups of the gods do not bother listing each deity's alignment. I doubt Greenwood resents the concept of alignment per se, but it just doesn't seem important enough for his setting to warrant the use of the symmetrical, alignment-based Outer Planes of the Great Wheel.
While the World Tree is underdeveloped in comparison with other D&D cosmologies, it also means that it's easy to take the model in any direction you like. Like the World Axis, the World Tree dispenses with a precisely defined number of planes in favor of a loose and flexible structure where you can place just about any alternate dimension you need within the model, or delete any concept you don't care for. The World Tree and the River of Blood, connecting the higher and lower planes respectively, are pretty useful and fairly evocative concepts to have. Finally, the World Tree avoids some of the conceptual rigidity of the World Axis, such as placing the Nine Hells in the higher realms of existence of the Astral Sea. Of course you can justify that in any way you like, but if literal Hell is not metaphysically "below" the mortal world, I don't even know what we're doing here anymore.
Those are my reasons for favoring the most disliked or just plain ignored cosmology for the Forgotten Realms. I guess I am a sucker for the underdog.