Conceptually, I much prefer a game where my choices make a difference in the long-run. It makes the choices meaningful. So, in concept, I much prefer having some areas of specialization which allow more strategy and planning. In the ideology system, unfortunately, it is sort of a free for all - I would want them to be mutually exclusive, but would prefer if you have more points in one ideology, then the other ideologies cost more.
The game really does need something to make choices more meaningful- not just for a few turns, but for the rest of your game. Civilizations make choices that effect their futures. So, again, in concept, this is a good thing.
I think the problem is that, as it stands, there are too many specializations, effectively cutting out a decent chunk of the tech tree. Also some specializations, it would seem logical to be able to just invest more time and then figure it out rather than be unable to do so. However, I do think there should be researches that are mutually exclusive in order to make the choices matter.
I am not in favor, at all, of a sandbox game in which, in the end, I always pretty much end up with all the same things every time.
In the end, I think this thing needs a bit of balancing.