Now one thing that is insanely good about using 31 as opposed to 40d is that with castes, you can now have an imperial faction with imp guard AND space marines. Orkz will also be enhanced, with most spawnings (might have to make them egg layers?) producing boyz, but some produce the special gitz.
Necrons will also be good with the next update. Maybe be able to turn people into other necrons (pariahs?) as well as having several tomb spyders using 'necromancy' to make more necrons. Would be even better if they could be turned into the HFS.
So ideas.
Tau and Eldar take the place of the elves. Trade same seasons, tell you to do things and get angry if you don't. Imperial factions trade two seasons maybe? Dark Eldar take place of kobolds, maybe make them convert night spouses.
Custom workshops for Imperium definitely, but most especially one to turn ALL body parts into meat (soylens viridiens), remove artifacts.
Now if you do go the idea of having the Imperial forces be multiple groups at one time, I would suggest that you use different caste professions for each. This was something I didn't know was possible until I posted on the forum, but you might have a better idea of how to mod than I did
When siege engines get updated, they would be really useful for heavy weapon's teams, but maybe for now have one weapon skill for small arms and one for heavy weapons.
Edit: I would like to point out that I was making my own 40k mod, and I too started with the tyranids. Simply because they are the most challenging to mod it and anything after would be easy.