There are a couple of changes in the v0.3 build that will add depth to factories.
First they will no longer be built directly by you, instead each territory will automatically build their own factories. This will reduce input spam for the player.
Factories will no longer cost cash to build, instead they will build slowly over time based on your national construction speed.
With the introduction of commodities, if you have the factories but can't buy their inputs then they will sit idle. Industry will need to be developed in parallel with infrastructure.
Hopefully these changes will add a bit more depth than just insta spamming factories to get money.