I recently binge-watched a show in which the protagonists discover that what seemed to be a single mysterious enemy organization was actually two diametrically opposed factions. When trapped by one faction, they were able to draw in the other one and escape in the ensuing chaos. It's an idea that's not actually uncommon in non-interactive media, and RTS games will also sometimes have 3+ sided battles, but I think it could work for RPGs as well.
There was a thread recently about keeping the enemies in the first Pillars of Eternity game low-level. This approach is probably the most sensible for the majority of combat situations, where the party encounters an enemy or group of enemies, has a hopefully challenging fight, but ultimately proves stronger and defeats the foe. In order to save some power progression for sequels, you have to limit the power level of the player party, which in turn means limiting the power of the enemies. But what if, occasionally, you encountered enemies that you weren't ever expected to beat outright?
These could be powerful beings or monsters such as dragons, or antagonistic adventuring parties at a significantly higher level and with better equipment, or small armies of powerful soldiers, or some combination of all three. If there is only one such group in an area, the objective could be to hold out against them just long enough to accomplish some task before escaping (or before being captured and having to escape later). If there are multiple groups from different factions that hate each other, an option could be to lure on group to blunder into a rival group, setting up a big messy scrum where everybody's attacking everybody.
This way, you can still have a game story that includes powerful, dangerous enemies while still ensuring that the player party don't have to become gods right from the start. Additionally, the same types of enemies could show up as beatable foes in sequels, demonstrating how the party has progressed.