I would really like it if the upgrade interface (both the governer and the specific ship popup) gave you the TOTAL cost of upgrades as well as the individual cost. I would also like it to inform you if your planned upgrade is going to take you below 0 credits (possibly by turning red?).
Many have suggested this in past, as this was in Galactic Civilizations II, however, has yet to get any love in this version, it also doesn't let you pay over time at a higher rate or only upgrade ships in selected fleet either as the past game allowed.