I like what we have now but would also like ideology to better interwoven with other aspects of the game as the OP suggests.
1) Different invasion methods could effect Ideology (Core implosion lol, that is malevolent)
2) Certain researches/techs could provide tools but also affect your ideology.
3) When colonizing, provide 5 choices instead of 3, don't make them QUITE as obvious, and two of those choices give you a mix of two ideologies.
4) Certain proposals if voted FOR or AGAINST in UP should award ideology.
5) I'm not certain how, but culture, culture flipping, and certain aspects of diplomacy could also be affected.
6) When you meet a Minor Race, we should also get moral questions, just like when we colonize.