A few years ago the LDS church leadership was saying that the biggest challenge facing the church was dealing with the growth in membership. I may be out of the loop but I 'm not hearing this as much as I used to. Regardless, if it has not happened yet, it will, in my opinion.
Growth may not be as large a challenge as a few other challenges I see ahead for the church that it should deal with sooner rather than later for the health of the church and it's members. I don't see these issues as changes to church doctrine so much as changes to culture and operations.
Challenge - honesty and transparency in it's objectives, policies, finances, and history. I've blogged about this before so I won't belabor the fact but the days are gone when an organization that depends as heavily on volunteer work as the church can spin a web of half-truths to those it needs most to survive. There will always be the "faithful ignorant" and bland crowd that stays within the lines but the church will continue to drive away the talented, unique, intellectual, creative, and outspoken with it's current practices. These are the very people the church needs most to stay relevant and fresh and impactful to peoples lives.