First, if you do not have a "webmaster" (a person who has authority to delete things, to tell people to "knock that shit off," and whose job it is to regularly patrol this content), you can and will end up with an endless mess of duplicates, partially-constructed sites, Potempkin villages where a traveler might foolishly expect content, and swollen archives of irrelevant data jammed in as a backup.
Second, people invariably notice workflows and they have the brilliant idea that they can attempt to automate a lot of paper-pushing. This is almost true, and only becomes completely true if they hire someone who is a Sharepoint admin, with real chops. Now, administration will not want to invest in another FTE, so they will instead attempt to hire someone who is half a Sharepoint admin, and half something else, usually whatever their current needs are. This is akin to laying out job listings for part-time brain surgeons who are also world-class detectives when they're not playing musical venues; Buckaroo Banzai never answers this particular call, and you get left with some clunky, badly-implemented workflows.
Third, you must have someone else responsible for hosting, backup, and upgrade of Sharepoint. You're not doing upgrades often enough for you to be good at it. Similarly, backups and restores ought to be left to the people who are into that kind of thing. See #2.
Fourth, as much as you would like a clean separation between intranet and extranet, you will invariably get "requests" from Important People that such and such from some other organization have access and can collaborate with some of your other internal intranet users (which ought to be redundant but now is not). You must recognize this from the beginning and plan accordingly.