Ship upgrades

[Major Marler]

What are the areas I should upgrade on the ship? In what order?

[Galdred]

Move first (and reactor when you want to increase move), Prognosticars at least to level 1 early, then more once you unlock the whole map.
Geller field is also great, as it lets you ignore warp storms.
These let you reach more missions in time.
The other upgrades are not that critical. You'll probably want barracks 1, cyber lab and medication chamber to not let your wounds/deaths go to waste.

If you play with the latest DLC (execution force), you can postpone turrets, otherwise, it is good to have mid game, to let you engage plague ships for free reqs.

Shields last, but you should avoid getting to 2 hulls or less, so you can increase shields at these times, rather than pay for repairs.

[JPLRocket]

Repair all broken things. Then augmentation chamber and warp drive, all the way to maximum, improving reactor as you go. Then geller field, then surgical augmentics.

Begin upgrading guns, and switch to the frigate drive once you get it.

Prognosticars will get shut off in the mid-late game for 60-120 days, so aside from repairing the first, skip these until after that happens.