It would be great if there was a way to enable modules within the mobile templates. It is great that this tool makes a site mobile friendly but when it strips out modules, it effectivly strips out important content and menus that are critical for some pages.

If we had some way to include modules somehow that would be awesome!

Hi,
The way to get the modules to show in the mobile template is to make a copy of them, and publish them to a position in the mobile template.
In Joomla 1.5.x
Joomla backend admin
extensions > module manager
make a copy of the module (tick in the box and click copy on the top right of the screen)
in the copy, edit it so the position is mj_all_middle
save
you should now see the module when viewing from the mobile.
You can make multiple copies of the modules if you need a location in the mobile template which is not common (shared) by all such as mj_pda_footer2, mj_imode_footer2, mj_iphone_footer2
Hope that makes sense and is what you were looking for.

Thanks, learn something new every day...

hi

is there no way to enable plugins/modules inside the content?

This is just like adding any module to Joomla content. Create the module and set it to a position that is not part of the live template. So if you create a module and set it to a position called joomla, then you go to the article you want it to display in and call it to the article like this {loadposition joomla} and it will show up when that article is displayed. 

NOTE: Make sure to publish the module to all menus otherwise it may not work.