A thought regarding the apostacy

I have been spending a lot of time with the missionaries these days. This has given me plenty of opportunities to particpate in the lessons they teach. It has been very rewarding. Recent changes in the lesson/discussion structure has included the apostacy and restoration as some of the first principles that people are taught. The first lesson, as taught by local elders, is longer and discusses more complex ideas then I was accustomed to teaching while an elder.
It was during one of these recent first lessons, or discussions or whatever they are called these days, that I was struck with a thought. Not a thought that would in anyway shake my testimony, but a thought that raised an issue that I don't feel has really been addressed. I am hoping that some of the occassional and silent watchers of this page- namely Bell and Gar- will help me with this.
We were at the point in the lesson where the apostacy and restoration were brought up. The elders were discussing what comprised a dispensation and what it meant to be in a state of apostacy. The next few minutes were spent teaching about the rejection of the early apostles and the darkness created by the apostacy. I got to thinking. According to our calculations and understanding of time, we have inhabited this earth for something like six or seven thousand years. (Gar correct me if I'm wrong) Why would the lord allow for such a long apostacy when that period of roughly 1,700 years would account for something like 25% of our existence on earth? That equals millions of people who never even had the blessings of the church and priesthood in their lifetimes.
It seems hard for me to think that a perfectly executed plan would include such a long period of time where there was little eternal progress. I realize that the millenium and temple work will help all of these people out. I also realize that, compared to the answers provided by mainstream religion, this one makes much more sense. This thought doesn't really shake my faith, it's just something I want to better understand.