there is no diffirence between calling the python interpreter and embeding the pyton intepreter , because in both cases what is executed is the python intepreter. So both approaches do not affect you in some way. Embedding python has advantages for the developer of the program because it creates a direct connection between python and the app that calls python. So you can use whatever library you want with blender python, it has some libraries removed to avoid conflicts but generally third party plugin libraries should work without a problem.
So embedding python has no effect on user , or even blender scripter . It makes a diffirence with blender developers because it makes it easier to wrap functions in c directly to python functions while the application is running. Other than that, is a normal python install.
The problem with using a gui will mean that you will have to create a new window cause eitherwise you will have to hack blender source code in some way which is extremely hard. Actually blender 2.5 gui is great and far from ugly, it can still improved but I am sure you will love and slowly learn how flexible it is.