Aside from fanboyism, it really depends on priorities. I've owned both Toyotas and VWs continuously over the last 10 years. I'll tell what the differences are based on my experience:
1. VWs are not robust to sloppy maintenance. Use the wrong oil and wrong intervals and it will likely cause premature problems (e.g. sludging in early 1.8T's, cam follower wear, etc). With a Toyota, a quicklube place will keep it running fine.
2. Given that you maintain a VW properly, it rarely has issues. I've had more unanticipated visits to the shop for my Toyotas than VWs. But the key here is proper maintenance of the VW. You have to do more research on how to properly keep it going strong.
3. The VWs just feel more premium. Close the doors and they feel like vaults. Close the Toyota doors, they feel like tin cans. The interiors are probably a generation ahead in the VWs.
4. When I take long road trips, I get excited when I drive the VW. Not so much with the Toyota. It's more like "what time are we going to get there?".
5. Which I would prefer to own depends also on where I live. Right now, I live in an area with very few twisty roads and my commute isn't very long. I also don't have a good VW dealer or indy shop nearby. So give me the Toyota. But if I lived in an area with good driving roads, it would change the equation.
So it just boils down to priorities.