Gotcha.
There are two questions here. One, is the basic game mechanism not a good idea. Two, (assuming we get past One), is the specific mechanic balanced (that is, is it simply a question of tweaking the numbers)?
Thinking out loud about One... The basic concept is that "more is better". I don't think we can get away from that. It's inherent in the game concept... you build your city and terrain infrastructure throughout the game, and as a result you have more benefits.
We could encourage players to build a little of all terrain improvements by giving each mechanism a penalty. Like how boreholes had a huge benefit, but also a penalty. So, maybe, if you cover your land with energy collectors, you get more and more negatives to your Planet value, or it has a bigger and bigger "drying" effect on the surrounding terrain (turning it arid), or something. Same thing with Forests, maybe it also has a negative on your Planet value.
Another way to proceed is to look at the alternatives. The problem (as I see it) with CIV is that cottage spamming is obviously good, but the alternatives don't really compare. In other words, if you got invaded and Towns pillaged down, are you likely to say screw it, farm over the land, and run specialists? Not unless it's the very end of the game... Almost certainly you're going to re-cottage. The reason for this is the civ-wide Civics. You're running Emancipation and Univ Suffrage. Specialists only really compete when you're running Representation etc.
But, SMAC doesn't really have this. The "Civics" don't really impact your energy income (etc). So, there's no civ-wide incentive to go "whole hog" in a specific strategy.
I think I'm concluding here that it's not the nature of the cottage mechanism that encourages spamming. It's the nature of Civics that encourages spamming. And, I think we'll probably already avoid that (because SMAC didn't have it). So, all we have to do is to "balance the numbers".
However, now that I've said all this, what SMAC does have is tech-based encouragements. For example, if you go the Morgan route, you get bonuses to energy. So you're encouraged to spam energy collectors. If you go the Deirdre route, you get bonuses to Forests (and Hybrid). So, you're encouraged to spam forests.
I think I'll stop here and see what everyone else thinks.
Wodan