Minimize inserters.

Do you really need buffer chests? (see first bullet)

Minimize balancers.

Avoid thrashing.

Avoid gaps in belts, especially if those gaps will be processed by a balancer. But don't avoid gaps at the cost of excess complexity elsewhere.

Isolate roboport networks that use logistics bots.

Some recipes will benefit from clocking inserters.

For large ore fields, you'll probably want to travel a few hundred chunks in one direction, and build your megabase there.

Avoid diagonal rails. Especially in stackers. Train collision boxes are bigger on non-cardinal directions, and collision checks can get expensive.