This is the first time I've really paid attention to customising Salesforce1 as these users are mobile field workers so will be using it a lot. 

• You can't have different navigation for different users. I don't want field users to be confused by reports and dashboards, but I do want Sales Users to have them.
• Please for the love of all that is worthwhile turn off "Allow Salesforce1 to import Contacts from mobile device Contact lists". No, you NEVER want that. 
• Ensure you hide the tabs in the profile for stupid things like Skills and Badges. 

Mobile Smart Actions

• Ensure you add Mobile Smart Actions to the Lightning Actions bar (see Record Home and Record Pages) unless you REALLY don't want to encourage Activities. See help doc for more info. 
• Ensure it goes after POST. 

Actions

• Actions are super mighty handy for mobile users - get them to do most things via Actions.