They just have to tell you it is a Super Project (1 per civ; permanent), or whatever they are going to call it in GC III. At the moment, the problem is that they don't tell you what is a Build Lots of on a Planet building, Build One per Planet building, Build One per Faction building, and Build One per Game building.  The latter two are usually permanent.  Once those descriptions are in, this should be a lot more clear.

Anyone played mass effect ?

The way paragon/renegade works in ME2 and ME3 is something like this;

You have reputation, which is the 'weight' of your choices so far, every choice you make, good or evil gives you basically the same amount of reputation.

If you want to make a special action, you need to have sufficient ratio of good/evil points...

So applying that idea to galciv, let's keep track of your  decisions and scale the costs of perks by 1/ideology ratio.

For example, you colonize a new planet and get 10 ideology points decision, and choose one. Up until now you have kept 60 ben to 30 prag to 10 evil ratio.

You can spend those points you just earned on ANY tree but you have to pay 1/0.6 of the cost for benevolent, 1/0.3 for pragmatic and 1/0.1 (10 times more!) for malevolent... Maybe even more penalty for the tree that is opposite of yours.

So, mainly pragmatic ideology can reserch both good and bad without extra penalty(ecxept ratio) but malevolent will have a significant cost penalty to research benevolent...

5/

By implementing this, you can accurately depict your civ ideology(say drengin would be 5b/20p/75m) and develop ideology traits accordingly. It would be easy to research your primary ideology, and you could get a few perks from your secondary... But impossible to max out all of them because of ratio cost scaling...

My suggestion is that rather than applying arbitrary restrictions to reduce player choices, do two things:

1.  Make the "value" of a ideology pick increase significantly as one moves up a particular trait line.   Then, the benefits of focusing will outweigh the benefits of picking from multiple ideologies.   There could also be synergy bonuses --- as you increase the number of picks in a particular tree, the following picks have reduced cost.   That makes intuitive sense to me, the more good I do the better I am at being good.

2.  Scale the ideology cost vs.  the game size and number of players in the game.   One possibility then is that finishing a full tree will be nigh on impossible.

Combined the result will be that most of the time focusing will be better, but the player has a choice.  

EDIT:

Essentially the same as the ideas (more fleshed out) in the link in the previous post.

No, it looks like I was wrong about this.  Either that, or it's been changed.  Now it appears that whatever you have the most ideology points in is what you ping as.  I think it might be only the ones you've spent points on and not the ones one has stored up, though.

Either way, I can now confirm that ideology (for diplomatic purposes) can and does change during the game.