It’s right that the vision and design principles are very different from TW despite the similarities. In that regard I’m more inspired by the Combat Mission series than TW:
bonuses: should ideally be an emergent behaviour as the result of simulating lower-level physical and mental processes. E.g. why do cavalry have a “charge bonus”? Because of their momentum, i.e. speed and mass, which are physical concepts. The current simulation model supports this to some extent, but the model is very simple and needs to be refined.
upgrades: adding support for modules and moddability (i.e. new eras and units), it will be possible to have many different unit types and unit variants. With support for army customization (choose your units at the start of a match), this will roughly correspond to the conventional “upgrade” functionality.