Titanium Alloy basically follows MVC (Model,View and Controller) framework with support of backbone.js and underscore.js where as in Classic structure there is no MVC framework.
In Alloy structure, we can write the code for ui and implementation differently in different files whereas in Classic structure we write code and ui functionality in single app.js file.
Alloy structure contains the folders for Models,Views and Controllers in which we can add our code in that particular files.Whereas there is no folders for Classic structure.
Here are my two cents. While Alloy is the main direction Appcelerator wants the Framework to go. There is absolutely nothing stopping you from using classic Titanium as your code base. Keep in mind that while it is easy to create mobile applications using Titanium, it is also very easy to generate bad code that don't abide by any design pattern. It is my understanding that Alloy, by forcing developers to follow a certain path, can do some of the heavy lifting for you. (releasing objects from memory, generate requireJS code, etc.) Hence being a huge gain for medium to low-level developers.
Of course, for developers like you who have deep knowledge of the framework, Alloy brings much less value to the table. That's kind of the same old debate between managed code (like Java or .NET) and native code (C or C++). Both approaches have their advantages and their faults. For example, native code might perform better, but it is more prone to memory leaks and bugs if the developer is not highly skilled. (you see where I'm going with this...)
In conclusion, I think that Alloy might actually improve the overall quality of many applications since not all developers are highly proficient with Titanium (as you are in this case). But I think that using the classic approach (that will always be available btw) will always provide more flexibility since you have full control over the code base.
As I said, that's my two cents
