Hi Steve,
I just thought of something based on my own conventional campaign - you'll probably want to look into a "tech offset" in NPR generation for your conventional campaign.
In my campaign, it took me roughly 15 years to get out of the solar system. This was with "hacked" (50%) costs for construction factories and mines; I suspect that a normal campaign would take closer to 20 years. In addition, I focused pretty heavily on economic development and military, plus I had plenty of minerals. I suspect that your campaign will focus more on military (leading to an even longer "exit time"), plus you might have a mineral crash before you get out-of-system. So it's not unreasonable to believe that your campaign will take 25 years to begin exploring the neighborhood of Sol.
As you explained in 4.0b, the tech points available to an NPR at generation is proportional to the time since the game's start. My first NPR was encountered only two jumps from Sol, and they are vastly ahead of me in terms of technology. For example, they're using MHD engines while I'm still on Nuclear Pulse. I expect that all the other races I encounter are going to be similarly advanced. At present, the only way I can think of to avoid being squashed like a bug is to make friends with them and try to get them to give me technology (I don't remember if this happens at high levels of alliance or not).
I have two thoughts on how to avoid this situation:
1) During startup, allow a tech offset to be specified, e.g. 20 years. This offset would be added to the start date for the purposes of NPR generation.
2) For each starting race (player or NPR), remember the date of 1st jump. When a race discovers a new NPR, use this date as the start date when generating that NPR, and pass the date along to the new NPR as that race's 1st jump date.
One more thing I'm having trouble with on the NPR AI front - I don't know how to declare ownership of a system or body to a neutral NPR with whom I've established communications. After discovering the NPR 2 jumps out, I withdrew to the middle system and picketed the WP with a scout with active sensors blasting away. This system had a habitable world on it; I was going to put a colony on it, but realized that that would hurt my public's opinion of the aliens if/when they came through the WP. Eventually they did come through the WP, and were picked up by my active sensors blasting away. Rather than recognizing this as a claimed system, however, they sent through a bunch (7) of colony ships and proceeded to colonize the habitable world. (BTW, they didn't have to geo-survey it before colonizing! I understand that this makes life simpler for you, but it seems a bit unfair.) I suspect that this is what's always going to happen - when they discover my home world they're going to charge into it as well and start grabbing territory. The thing I'm concerned about is that I suspect that this is the only behavior NPR will exhibit - I would rather have them make a random decision as to whether they're going to ignore existing claims to a system or avoid contact and leave (or at least not colonize) if they discover an alien presence in a system. From a game mechanics point of view, it feels like there's always going to be a war, since they'll eventually colonize my home system (or even home world) then get all paranoid when they detect my fleet.
OTOH, this dynamic of them barging into systems that I consider mine and me being concerned about their territory grabs is certainly exactly the way a lot of historical wars have started - if the tech differential weren't so big I suspect I'd be a lot less concerned about it.
One thing I haven't tried (didn't think of it) is declaring an exclusion zone. I don't know if these are still active or if aliens will pay attention to them.
Thanks,
John