At risk of being the 'new guy with an unpopular opinion', I think they should just remove nukes all together. I mean, I kind of foresee it going one of two ways. Either Uber does nothing to correct the nuke problem, and we continue with what we have now, or nukes get 'balanced' which normally means they're nerfed in such a way that they're not really useful at all. In the real world, nukes aren't really weapons so much as they are threats. Countries have them to have them, but they've only really been used once. More over, using nuclear weapons now would likely result in either similarly heavy handed retaliation (ie mutually assured destruction) or serious geopolitical ramifications for the user. Which is basically why they've only been used once. The problem with a game like PA is that it's, well, a game. They're no real negatives to using nukes on one another, and since they're literally the 'best' weapon, they're no reason anyone wouldn't want to use them. Why reach for a tiny little peashooter, when you can grab a machine gun? I'm just not sure nuclear weapons can be balanced in a game like this. As for turtling and similar, part of the reason I rarely build too many factories is because, in general, factories are expensive. Not necessarily in terms of metal or energy, but in terms of ground space. I find it difficult to place them anywhere except in rather strange locations (much of the terran, which appears to be clear, isn't or something bugged as it were) and given the cost of the factory, it's difficult to take the risk. If factories were dirt cheap, I mean really dirt cheap, and smaller, perhaps people would spam them since there'd be less of a problem placing them, and it wouldn't matter as much if you lost them because you didn't build proper defenses.
But they are also expendable given the mass, energy and time investments. So you can balance them and their counters nicely via relative numbers. Such as 37 heavy tanks are the perfect match for 13 turrets - number totally pulled out of thin air here. With nukes you do not have that latter luxury. Since they are quite the monsters - by design - in terms of both potential impact and upfront expenditure they tend to arrive to the party in very low numbers at first. One by one, most often. Add to that the symmetric nature of the nuke mechanics that lead to offense and defense coming to the field and cancelling each other out at a ratio of 1, give or take. Which makes balancing them and their counters really hit or miss.
Follow that logic then. The conclusion is that you have to reduce the binary nature of the system. Make anti-Nukes hit and detonate the Nuke mid air, scramble the Nuke's guidance so that it nose dives in a random direction. Have nukes with hitpoints so OTHER units can take a pot-shot at them as they fly overhead. On the flip-side you can make Nukes come in various different flavours. The obvious one to try is having both a tactical nuke and a strategic nuke... maybe even dummy warheads that can spook your opponent into re prioritising into defending an attack type that will never really come, and assaulting him with ground forces as he is scrambling Nuke defence. There's so many easier and gameplay intuitive options that would take advantage of pre-existing systems that should be considered before you start reaching for additional and unituative solutions, like your nuclear fallout suggestion on page one.
I preferred expanding on the existing suggestion since I already stated my dislike of the current system on occasions before and did not want to simply reiterate here instead of taking up the ideas of the thread. This does not change the fact that bringing inherent balance to the system is more elegant and beneficial, though, so your proposition brings more to the table than mine and should be looked into.
I think that's the trouble with forums. Perfectly reasonable ideas get buried fast and the outlandish suggestions start to spiral out of control. I find the thread title oddly poignant at this time.