A preferences option in Avogadro would be great. Ubuntu Linux derivatives with gnome or Cinanamon GUI have font adjustments, but none modifies the Avogadro GUI.
Check if your account has a folder called bin, if it is not there, create it. In most linuxes if you create it, or if it is already there it will be recognized from anywhere in your account (if it was not in your account you will have to log out and back into your account after you create the bin folder). In bin create a text file (I called it avo) to do that move into bin and type
touch avo
chmod +x avo
with your favorite text editor (vin, gedit, or ani other) and type de following into avo:
now if you type avo and return in a terminal window, you will have avodaro2 running with large letters in the GUI. Now avogadro2 looks like in the printscreen annexed
If you edit the Avgadro2 icon in /usr/share/applications (must be root to do that) to point to the avo file (/home/csevcik/avo in my case) clicking on the Avogadro2 icon will activate the version with larger text in the GUI. I include a sample from my machine)