Writing this post is like opening a can of worms. What goes without saying for one might annoy the other. So this again is no absolute truth, just some topics worth thinking about.
Waypoints - Nice and informative, but very annoying for iPhone users. Normally I would only use them in cases where it helps creating a logical route or when an area has low portal density.
Waypoints & portal sequence - When using a waypoint next to a portal, keep in mind that a waypoint has unlimited visits while a portal has cool down. The best sequence for nearly overlapping actions therefor is: first portal hack, then waypoint visit. This way one cannot hack the portal, before visiting the waypoint.
Passphrases - They can be as helpful as they are irritating. The ingress UI makes it very unpleasant to answer multiple passphrases in a banner. On the other hand, in an area with lots of missions, it makes the next mission easy to find. Eg. the last (hacked) portal of mission 12 can be reused for a question when starting mission 13.
Wrong passphrases - Having passphrases that require searching the web make for more dislikes on your missions. Having questions that trigger exploration of the portal and it's surroundings are challenging, but if done right a nice add-on. Never rely on the portal description for that, as this is subject to change. Ideally you can use multiple choice instead of open-ended questions.
Passphrase sequence - When you do use the hack-passphrase sequence described above, then use that sequence. Some say it's nice to ask for the number for the next missions on the last portal, but people who, like me, like to hack-and-go, have the chance of hacking before the question pops up. This requires a heat sink at the start of the new mission. Something that can easily be avoided by using the hack-passphrase sequence, instead of the passphrase-hack alternative.
Also check the post on Aspects of a good banner for more tips and tricks.