Factions can be there for two reasons. Either story forces you to have them, or they exist to give the game more content.
If youre not forced to have factions, I wouldnt have them. If you want to give players a big "A, B, or C?" decision, just do it at the beginning of the match based on for example what type of factory the player builds as the first production building, or a similar big choice that you cant really undo or youll be weakened.
Importantly, doing it ingame allows for more possibilities. Ingame, you can easily combine many decisions to give a ton of permutations (do I start with two tank factories, or one tank and one robot factory, or one plane factory and then save the remaining resources for later etc.). With factions, you can have only so many (=very few) options until it gets messy, AND its probably a lot more work for factions anyways, because you want them to look different and so on.
In that sense, choice of faction is no different from any other gameplay decision, except its usually costly for you to implement and balance, and offers very little extra depth to the game in comparison to adding some other game mechanics that offer far more options for far less cost.
Basically, if you COULD make factions be a decision of which is the first building you start with, do so. This gives you the freedom to make the system more interesting. If you choose your faction from a list at start of match, its very difficult to expand on the system. If you keep it ingame, you could lets say change faction midgame. Or belong to 4 factions at the same time at endgame. Treat it as not being different from other game mechanics.