For me, the whole process of becoming aware of the imperfections and human frailties in the operations of the church (historically etc.) has been a tremendous opportunity for personal growth. It has helped me remove some of my pride, become somewhat less judgmental, hopefully a little more forgiving, focus more fully on love and the essentials of what Jesus taught. For me, becoming aware of the humanity has helped me progress out of a spiritual plateau that I didn’t know I was in (yes, first by crashing down but that is another topic).
If the purpose of the church is to help us progress spiritually - to help us grow personally, I can’t think of anyway that I could improve on its current composition to help it fulfill that goal (at least for me personally) more effectively than it is currently doing for me.
One big step was realizing that in learning to forgive all men (D&C 64:10 - not condone but forgive) I needed to forgive those in the Church who came before me for any mistakes they may have made.
It is the resistance we encounter that makes us stronger – wherever it may exist.
I want to add only that we sometimes lose sight of how radically different the stated goal of Mormonism is than any other Christian religion. (Buddhism's ultimate objective is similar, but that's another topic.) We talk of a literal and extensive conversion of character - of becoming fully something we now are only partially. Compared to the more "mundane" goal of mainstream Christianity, we really are radicals and extreme liberals theologically. I think that's important to recognize and admit openly - that we have a radically liberal theology, taught within a generally conservative organizational structure (mixed with quite liberal elements, like a lay local leadership).
The things that bother me most about the Church are the more mundane aspects of organization and the interpersonal conflicts that inevitably arise when people with different perspectives interact and strive for unity. The things that inspire me the most are the visionary aspects that still blow my mind on a regular basis - the fact that such flawed people still could articulate such a mind-blowing theology and cosmic paradigm. It reminds me of the founding of the United States in some ways - some really flawed people who couldn't live the ideals they wrote (e.g., in theory "all men are created equal" [except in practice for slaves, who only count as part of a man for census calculations - and the women, who aren't even mentioned directly]) but who still created something great and incredibly liberating.
I'm not sure if I would phrase it like my friend did when he sent the message ("The Church's Flaws Make It True") - but I absolutely would say that the Church's flaws make it real and powerful. Maybe, in the end, that is the same thing as "true and living" - perhaps defined as "not artificial and able to grow". In the end, I still define "true" as "pointed in the correct direction" (like "true north") - and, since no other major religion (other than Buddhism) of which I am aware posits what we posit as the ultimate objective and purpose of life, I feel fine using the word "true" in that sense.