OK, there's more than two, but these two seem to be fundamental to the way I use the software; fixing them would go more than halfway to getting the mobile app up to speed with the desktop app.
1) Lack of ability to use saved layouts.
Having used the desktop app since L3, I have come to rely on saved layouts to save time...a lot of it. It can take hours, over multiple sessions, to get a study layout to a specific design that works "slicker than snot on a doorknob" (as my late Dad liked to say). Having to try to recreate these on the mobile app greatly dilutes its usefulness. It's almost like Logos thinks users of the desktop won't care about the mobile app and users of the mobile app won't buy into the desktop app. As Lee Corso likes to say, "Not so fast!". Integrating these saved layouts into the mobile app would be a huge step forward.
2) Lack of ability to make clippings.
Logos isn't really 'Bible software,' it's more 'library software.' Maybe I'm a fossil, but the primary way I use a library is to find information, clip it (figuratively), and organize it for use in a project/paper/lesson/sermon. The inability to do this simple process using the clippings docs saved in the user account will continue to make the mobile app a third-class citizen in the Logos environment.
Logos, please put some time and effort into integrating these essential tools into the mobile app.