I'm not sure how exactly the point costs for each element of the ideology trees are calculated, but I believe the more you spend in one tree, the more expensive other trees become. This is, in some ways, a means of dealing with the differences in ideologies (i.e. the more invested you are in an ideology, the easier it is to go down that path and, conversely, the more difficult it is to go down the others).
I'm okay with this, to a point, but I do think (and have posted elsewhere) that some of the ideology elements are mutually exclusive.
Doing this would require that the Ideology groups be less pyramids (you currently have to buy everything on a level to get access to any of the stuff below it) and more trees (where losing access to a ideology entity only cuts off that branch).
I think this would make decisions much more meaningful--if you can have everything, it is less about which to choose, but rather which to choose first.
Sorry for the wall of text, but . . .
Another issue I have noticed relates to the improvements that are made available through the ideology tree. First, I really like that improvements become available as ideologies progress, and I like that the buildings offer points toward ideologies. This does create a ripple-effect though: as you gain a new ideology-based improvement, you can much more quickly progress through the ideology trees.
Even in a tiny map, you need only unlock the first level of each ideology through colonization events and anomalies, and then you can use buildings to progress in all three ideologies. And because points don't disappear when you destroy buildings, this is highly exploitable.
I realize something may already be in the works to improve this, and that the point values and other factors may be in place to help speed things up during alpha, but within about 150 turns, I've been able to unlock all of the available ideological elements. I think that either the buildings need to be less generous in the number of points they offer (and perhaps fewer unlocked element should grant new improvements), or the individual ideological elements need to cost more.
Also (and I'm not sure how this would effect gameplay--it may be a terrible idea), I think that destroying ideological improvements on colonies may need to also remove the awarded points, and any unlocked elements may need to become re-locked (in the order they were unlocked) if the points drop below the required cost to unlock. I don't think I would have a problem with this in terms of gameplay if I was notified before destroying an improvement that such an action would remove an ideological bonus.
So to summarize--
If a player can unlock all the ideological elements, ideological choices are pretty much meaningless.
If there is no loss of points when an ideology-based improvement is destroyed, players will likely destroy and rebuild these improvements to spam points in the desired ideology, thus totally undermining the value of making meaningful ideological choices.