Which, coincidently, my roommate and I were talking about just yesterday.
We both agreed that when we think about "the institution" of the church, there's enough there for either of us to just pick up and leave the church (with a bad taste in our mouthes) at any given moment. That being said, we discussed how spirituality is about individual communion with God AS WELL AS gathering with a fellowship of Christians -- that there's something about coming together with others, with "the body of Christ," that is absolutely critical to the experience of God (a lot of things actually but that's a topic for another day) So, to us that's part of why choosing a religion to gather with is so important. Every institution of any church is flawed -- but they all offer an opportunity to come together as a community, and community is important.
As I've gotten older however, I've realized that some communities are better for certain people than others...and many seem to be called to the place where they can find God in a way that fits them. God knows us, and if we are seeking Him, He will guide us to the best path for each of us individually to find and know Him. To be honest, I am not always sure that being part of the modern mormon community is the best fit for me... I have always sorta been on the fringes -- too stubborn to conform to the culture and always asking controversial/disconcerting questions. BUT then again, maybe that is why it IS a good fit -- it has been a challenge in many ways, and a rough stone needs to roll through rough terrain to become smooth...
That being said, what it all finally comes down to is this: The personal relationship that I have developed with God through belonging to the LDS church is the most precious things that I have in my life -- and it has been belonging to the LDS church, with its strengths and weaknesses, that this relationship has come; the doctrines, the experiences I've had (good & bad), the quirks of the culture, the people (wonderful ones & difficult ones), the inspiriting as well as terrible history -- everything is a part of me and has shaped who I am…... and it has also provided me with the opportunities to know God.
To me, that is a "true church" -- one that is bringing me to Christ -- so, because it is true for me, that is why, despite (or perhaps even because of...) doubts, discouragement, contradiction, hypocrisy, etc. I choose to stay.