I'll agree that the basic damage repair upgrades are highly worthwhile early game (at least before you can get the repair cruisers), but the first upgrades I'd ever suggest anyone get outside of those are some of the anti-matter upgrades. Granted, not too many of them. I find that upgrading thru all 4 levels leaves most ships outpacing any of their cool-down requirements. These mid-game upgrades definitely help your capitals and cruisers. With ships, upgrade just enough to where cooldown is your ability-limiting factor and not antimatter. I can't argue the hard math for it, but when your Kol can flak burst AND gauss cannon as fast as the cooldowns permit...well, that's a heap of space-born hurt.

But aside from the early game repair and mid game anti-matter, I really would spend money on more ships first. More to be said for having a huge fleet first and then upgrading it. Sure, each upgrade makes each ship a better value, but each ship makes another target your enemy must consider how to handle. Each ship also has a seperate rate of fire and repair. Someone who upgrades early simply hopes the enemy doesn't come charging down their throats while waiting to build their own fleet.

I've only played a few AI games, and got this lesson taught to me by a random pirate raid. But the same could be said with any game where production is limited by supply and upgrades are available (StarCraft, we're lookin' at you).

I personally am an eco guy, so I get one of you guys to protect me, then I do all of it in one big whoosh.

I get the first shield/armor upgrades after I've built enough ships to reach the second fleet logistics cap. Where upgrades get more efficient is that not only do they improve the survival of your current fleet, but all future ships you build. Weapon upgrades I tend to hold off a bit longer, they usually wait for prototype research.