So here's a very crude representation of what I'm thinking of:
![Image](http://s28.postimg.org/9ci642pkt/Factorio.png)
So an add-on building would add a bonus to the building it's attached to. Thr bonuses would come in two tiers: the first one available from the start and the second one would be something that has to be chosen from two available options after some additional research.
For an example, in this picture there's something attached to assembling machine. The initial bonus that it could give is an additional slot for a module. Then after some research you could choose whether this assembling machine should be able to craft two products simultaneously (so basically now it acts like two assembling machines) or if it could be used to make very advanced products that require 5 or more ingredients to make. This also means that both choices would be useful depending on situation.
Similar add-ons would be also good for buildings like oil refineries, robo ports, chemical plants and so on.
I think this idea would add more depth and complexity in the late and very late game.