- Caves for hiding resources from radar, and requiring advanced water pump tech to keep dry while electric/thermal miners work underground.
- Waterfalls for moving water, that drives watermills and in turn drive your mechanical empire and devious defenses.
- Wind for blowing away your enemies. No seriously, wind farms. And to be ludicrous, supplying oxygen for cave exploration and soda pop.
- Hills, to give reasons for building defensive alcoves or gauntlets or for better radar reach. For constructing restrictors/thumpers (Half life 2) to drive biters away. Or light beacons to attract their attention.
- Valleys, the really deep kind that require us to build bridges. And all associated tech that goes with building it.
- Earthquakes. Obviously, this one could get out of hand, but imagine having to earthquake proof all of your sensitive buildings. And it can be done.
- Bees. Bees need flowers, flowers need cultivation. Bees make antiseptic and sickness killing honey. For when you get a disease from that poisonous worm, you know the one I'm talkin bout.
All of the above suggestions are based on creating scenarios that force the player to use alternative tactics. Sometimes with the intent of using older technologies to overcome problems that prohibit advanced technology. e.g EMP pulsing prohibit the use of electronic devices, be it furnaces, solar or radar, but allow wind water and thermal (heh probably not this one).
Factorio's developers are ingenious. I see no reason It can't be expanded to include vastly improved environmental hazards, that drive the single player experience skyward (haha).