Or change to multiclassing rules to cover more niches (not that 5e requires them).
I'd especially like to hear about rules you put in play, and if they worked or didn't
Well, I'll be more direct this time since I have the time to write more.
I am currently running an online game with only two players and for
that game, I have an NPC, but he (literally last session) just died. The PCs are level 4 now, so if they want to try to bring him back (that is the plan), cool, otherwise I will probably have a new NPC-type (scout, dwarven mage, etc.) based on NPCs from the monster manual that are there for that adventure. Once the current story arc is done, the PCs will move on and I'll throw in a new NPC, etc.
In our CoS game, in which I play, we use two characters each for two players. Not suggested for novices, as you are aware, but it works and might be an option later on?
In our main game, at one point with two players moving away, another tied up with family, we dropped down to just the DM and two players. He instituted old-school multiclassing which I mentioned earlier. It is a stronger option, however, and I am worried the power-level might lead to analysis-paralysis with novice players. It does however allow you to cover the niches (if you want to) and you won't see much crazy synergies until level 10+. We have more detailed rules for determining hp and some other things, but nothing too hard to learn, even for novices (we've since had a novice join and he handles it just fine).
And, of course, as others have suggested, have fewer/weaker foes to match the PCs being half a party.
FWIW,
all the above suggestions can work fine IMO and I've never seen much issue with any of them. I've played in them or DMed them. My advice would be to just talk to the players, present different methods for dealing with only two players, and go with what everyone thinks will be the most fun.
