Will there be possibility in Unity to change default file manager?

One nasty limitation of upstream gnome is that Nautilus usage is hardcoded in, for example, in Gnome Panel. That causes Nautilus Elementary to replace nautilus package and nautilus executable instead of creating separate project. This also prevents users from using alternative file managers such as Pcmanfm.

Maybe Canonical should develop some measure to allow user to choose his file manager in Unity?

You can already change the default file manager in GNOME, although the setting is hidden.

Press Alt+F2 then enter gconf-editor.

You then need to edit the /desktop/gnome/applications/component_viewer/exec key to the command for the new file manager.