I see the same tendency for the lower branches to outgrow the top. I suppose what you do about it depends on whether you ultimately want a bush shape or a standard tree shape, and whether it's growing in a pot or in the ground. Others may have different opinions on this, but I always assumed that more branches and foliage meant more photosynthesis, which would mean more energy going into root growth and fruit. To me, more branches near the ground means more fruit within easy reach.
On slow-to-get-started varieties like Black Madeira I've left just about every branch it produces, in hopes that one will turn out to be a runaway grower that becomes a main trunk. If I think there are too many suckers and/or low branches, I just think of them as opportunities for future air layers or cuttings that are helping build a strong root system before I remove them. If a lateral branch outgrows the main leader, I'll likely keep the more vigorous part and remove the former leader. Since I'm more concerned about fruit production than aesthetics, I don't mind a trunk that isn't straight at the base.