Well, I don't want to set much in terms of rules on how people do this. Much of the thinking behind this is that it supplies something people can pick up, play, and then repost so that the game eventually winds up getting finished and that you can follow to some extent as it goes along. AI War is a game of interesting decisions, and I think the interesting decisions resulting from starting up at a random point in a campaign that someone else has been playing previously are pretty appealing, especially combined with the fact that it lets you probably avoid the start of the game (which isn't necessarily the most appealing part of the game to everyone). This also lets you play something substantial for a few hours while still making a real contribution to a game if you don't want to commit to a whole campaign. I'd love to see games geared toward multiple players, too; would work great, especially for those of us on IRC who could just play an ad hoc mid-campaign game when people have an hour of free time.
If people want to do it more in-depth where there's a real community effort to every leg of the game, then they're certainly welcome to it. If they just want to pick up, play, and put up their updated version for someone else to do the same to later, that's great, too (and more in line with what I'd been expecting initially). The former is probably more than I'd be willing to do, myself, in a game I'm participating in, but I'm sometimes rather lazy and also often busy with other things.
I'm also interested in just grabbing a save at some point and playing, putting up a new save when I'm done. I look forward to the interesting circumstances it'll put me in that I likely wouldn't be in if I'd been playing from the start myself.
Regarding my choice of fighters, I chose them because of the bomber starships, cutlasses, and cruisers that mad bombers like to send. Honestly, even mark I-III, I wish I had even more of them. Mark II cruisers don't seem all that necessary at the moment because mark I is capable of taking out the bombers being sent against me quickly enough. The raid starship is there much for it's ability to take out things underneath forcefields, which I've been seeing on enemy worlds. The special ship is deflector drones, a ship type I much love and which is pretty powerful in general against mobile military units. It's also rather fast and has a large range and high ship cap. It's definitely a good bonus ship type.
In this game, I have a lot of interest in getting the worlds next to the homeworld because of the buffer it'll create; mad bombers in particular are AIs I'm not comfortable having direct access to the homeworld. If you want to skip over one of those worlds in a game that's less structured like I had been expecting this one to be (though again, it's okay if it's different!), do so and make a note of it in the thread and/or on the galaxy map for that planet and hopefully people will respect that if they consider it viable.
As for making mistakes, I think it's great if we have to recover from mistakes and think it's wise to encourage people not to try to play optimally through reloading. Regarding losses, if someone is able to get the game to continue, then I think it should continue, though perhaps with losses noted in the thread. I think it'd be unfortunate for playing that's less skilled than necessary for the campaign to make the game halt in its tracks for those who'd like to see it continue.
Regarding patches, one of the awesome things about AI War is the fairly frequent updates and additions. As long as an update doesn't 'break' the in-progress game, I think that playing it on the most recent version is the way to go.