Manufacturing capability and redundancy. You can't just have one fleet machine shop, misjump that and the fleet is doomed to a slow death.
Simply put, the fleet is going to need to be able to rebuild itself over at least once. It should have the ability to mine asteroids and refine raw materials into compounds useable by the fleet. In fact, it should be possible for the fleet to build a shipyard from in system resources so that it can do major repairs.
So this means you need refining ships for raw materials, electronics manufacture, facilities for making hydrocarbons, "green" space for plant matter, etc.
The larger ships should have the ability to repair and replace the smaller, more at risk ships. It certainly slows down the trip, but otherwise you simply end up losing the mission.
Lose the tanker, fleet dies. Lose the shop ship, fleet dies. You also need the capability to create any and all food stuffs and pharmaceuticals for the population. The fleet should not bring anything they can't recreate from materials expected in most any system they encounter.
And they should be able to do this after they lose some important ship in the fleet. It's not a short trip, and things simply break or have bad things happen to them. I don't know if hulls are considered to actually "wear out" over time or not (through micro-meteorites and other ablative space dust stuff). If hulls DO where down, they need to be able to manufacture and repair the hull plating materials.
I would in fact build 80% of the fleet, and then let the fleet build its other 20% to ensure they have the expertise and skill necessary to do it in deep space, this lets you test the project in friendly waters before you commit it to the void.
Much of the materials can certainly be prefabbed and stored on the ship themselves, but that will just speed early repairs but not necessarily mitigate the need to manufacture from raw materials. You can always repair with stores and then remanufacture to replenish stores.
Finally, the fleet needs to be diverse and reasonably scattered to prevent some plague from wiping the mission out vs a monolithic single ship.