Difficulty, operators, whitelists, MOTD, resource packs, gamerules and the server settings players actually notice.
Most of what people want to change lives in server.properties, and it is worth editing it carefully because a malformed line stops the server rather than being ignored.
The common changes are difficulty, making yourself operator, managing a whitelist and the MOTD players see in the server list.
All of these are editable from the panel on any plan. If you are still choosing one, see our Minecraft server hosting plans.