Let me know what you think, I'd be curious to know your thoughts. I'd also be interested in seeing a save file from that game if you still think something isn't kosher.
I expanded out at about that rate (It was less than an hour when my team mate and I got our second planets) and its how the game works, so I know there's no bugs, but I just think that, if you have more than one planet, losing one shouldn't completely wreck your game, expecially when you have a well built up team mate. I have an auto save from it, which is a bit before I rage quit ( 
), but I'll attach it anyway.
EDIT: I know technically I lost both my Posts, but I still say that falling into an economic stall shouldn't be that easily induced, and climbing back out again shouldn't be so hard.
Okay, looking at this save, it definitely looks like your expansion rates are perfectly fine -- well within the range of normalcy, not enough to cause any significant problems there. Bear in mind that I am looking at this in version V, which is a bit altered so it might be coloring my view of what I am seeing here.
But, at any rate, looking at it in version V I see you with 63k net energy, and Darkfox with 73k net energy. You've got 924 ships, and he only has around 700 or so. I notice he has a force field up over his home station and good wormhole defenses. Maybe a tad light on the tractor turrets for my taste and I think that force field over the wormhole is probably pointless since all it does is prevent the AI ships from escaping -- when coming in they pop around any force fields in their way, by design (and yours do the same if they have a force field in such a position). But anyway, that's looking pretty decently defended with not a lot of waste in either of your planets.
It looks like what has happened here is basically a critical lapse in early defenses, which let them take out one of your home planets. That's absolutely devastating, as you've said, and I don't feel like the penalties are too stiff -- if it is later into the game, it won't matter nearly as much, but this early in the game it is crippling because you are about to lose the rest of the way unless you battle your way back. In most other RTS games it doesn't even let you keep playing once your "king" or "supreme commander" is lost, that's just it and your allies have to keep going alone. AI War lets you keep going and you can still win as a team even though you are "dead." If this were Chess, you have basically already been checkmated. Losing any other ship in the game is not so devastating, but the importance of the home planet command station is such that it warrants extra redundant layers of defense over what you would put over anything else.
The waves of 1,000 or more ships is not terribly surprising at this stage in the game -- your turrets and tractor beams will easily dispatch that many if placed in groups of maybe 10 tractors and 40ish turrets. Some enemies will likely slip by, but you can still defend against that many ships without too many losses. When paired with the cloaking ships, you will also need tachyon beam emitters and some of the ships may still be immune to tractors, so in those cases you want to make sure you have force fields up around your home command station, plus lots of turrets over there to pick off the ships as they try to bust down that force field.
Then, the focus is getting buffer planets on all sides of your home planet, which it looks like what you were already doing.
Again, I'm looking at this in V, but seeing your current state I think this is not an unwinnable position despite the fact your home is lost. Yes you have a wave of around 1000 ships coming in once again, but they are autocannons and planes, which are not the strongest. When I was looking at it they killed your remaining command station once again, but then they went to your ally's planet and all died on his defenses -- and he didn't even have that many turrets up at all, only 7 mark I turrets inside his mark III force field over his home command station, and that blew through over 900 AI ships with his force field only getting down to 91%. He lost zero other ships with that wave.
So that then puts him at a pretty good situation, he still has 171k metal and 61k crystal at that point, and can easily give you a couple of colony ships to take those other two planets back and get you back on your feet with resources. You still have a fleet of over 800 ships come to that, so you've got a lot of muscle to move around during this same time, taking more buffer planets to keep them from raiding your still-resource-rich home planet quite so much. In another 20 minutes you could be basically back on your feet, with stronger defenses in place, and ready to aggressively expand back out into the galaxy with that huge fleet of yours.
Your ally would be in the hole resource-wise for just a bit longer, but then will also be back up to his full strength once you are settled with your two planets, and then you're both back on the offensive together.
In all, I'm not seeing any major deficiencies or imbalances here, it looks like the AI just caught you by surprise -- it happens. Of course, the resource view may be a bit different since I am looking at it in V, but that's the new current version.
