@Fonzo
To get the tech tree (.xls) please just email me (GSDioxine@gmail.com); I'll remember to include it into the update. As for the governments, the update will adress those issues; the large number of cities was meant as a special advantage to ecotopia which is sub-par in many areas anyway. The happiness penalty for large governments (60 or more cities limit) is 0.5 per extra city now, we might consider dropping it to 0.3 for 90+ city governments, so it would be less drastic.
Sadly, we can't do anything for easier loading aerial units; you need to use the sleep command for the units you want to load (building those airfields helps a lot, you know

). Hovercraft has a new, neat sprite already, much more real-looking, it will be supplied in the update. We cannot disable re-using of ICBMs for now, just treat their 2-tile non-orbital movement as them being transported by trucks or sth

. Aside from that, I didn't quite understand your problem. When launched at the enemy, it blows up properly like a normal nuke. Cruise missiles (non-nuclear) won't really work in CTP, in my opinion.
Whoa, it was a long post. Cheers, everyone.
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