Avoid custom master pages
Microsoft maintains control of a set of master pages, allowing them to regularly update Office 365’s ‘evergreen’ platform with new functionality. So, when you apply a custom master page to your site, even if it is an exact copy of an OOTB master page, your new master-page version will grow increasingly out of date. This popular graphic borrowed from a conference presentation explains it.
Just keep in mind that custom master pages are still supported, but not recommended, in order to minimize future maintenance. As a rule of thumb, you may consider custom master pages or web templates only for publishing sites, and avoid them for team or collaboration sites.
If you would like to learn more about the pros and cons of custom master pages, this blog post is a great resource.
Leverage Office 365 and SharePoint themes
One of the recommended options for branding SharePoint Online and Office 365 is using custom SharePoint themes. Themes allow you to define colors and fonts to support your corporate brand standards. For SharePoint sites, there is a tool for creating themes called SharePoint Color Palette, which provides a user-friendly way to generate a color palette file for your ‘Composed Looks’. This blog post will teach you exactly how to set things up. Unfortunately, SP themes, or ‘composed looks’, do not apply beyond SP for sites, such as One Drive, Delve, Admin dashboard, etc. However, Office 365 provides a rudimentary theming engine to customize the top navigation bar (colors, fonts, and logo) for everyone, everywhere.
Follow Office365 PnP (Pattern and Practices) development recommendations
Office 365 PnP is a community-driven set of recommendations, documentations, and samples to help you transition your development from full trust, on-premises solutions to SharePoint Online and the app model. I cannot emphasize this enough: download the samples, watch the videos, and read the guidelines (links below) before starting any custom development for Office 365.