I've got a similar problem with my album. I find that there are certain lines that have more personal meaning than other, lines that have more significant photos / memorabilia than other lines. I start with those major lines and go straight back.
Then I'll pick up another line and go straight back. If there are tiny off shoot branches I'll stick those in as well, but if it requires more than two pages I hold off for later. The lines might not always be near each other in relationship to each other, but it keeps each branch straight.
I also start off each branch with a title page/family tree to keep things explained and easier to follow. I used the pages below for that. You might also want to go ahead and plan for multiple albums if you have such an extensive tree (ie. father's side, mother's side, and nuclear family).