1. You generally underestimate the range of bee pollination. It is a lot larger then the area bees usually affect. Check the furthest distance away from your apiaries where flowers are being spawned by your bees. Now triple that distance, and go a few blocks further for good measure. Any tree in that (rough) area has a chance of being a target for pollination. On my server, the person who was doing tree breeding was complaining about nothing ever happening, only to hop over a small hill and find 5 pollinated leaves in trees on the other side, more than 2 chunks away.
2. Pollinating targets are chosen at random. First, a source leaf is picked to determine breeding partner 1, then a destination leaf is picked to determine breeding partner 2. If both partners are identical (two vanilla oak tree leaves) then nothing happens at all. And if your apiaries are standing in a wood of oak trees with just a few birch nearby, then most of the time nothing will happen. Therefore, you want to have maximum tree diversity in your breeding area. Plant an equal number of each oak, birch, spruce and jungle trees (4-5 each) and make sure that no other trees are in range. Once you have gotten a mutation, add the new tree to your breeding copse for even more diversity.
3. If you play on the 1.5.2 beta pack, treealyze your vanilla saplings before planting them around the apiaries. That way they have a genome, and trees with a genome have a chance to spawn butterflies. Which are not only neat-looking and collectible, but also randomly pollinate trees (they have a tendency to fly all over the world though, so you might randomly find pollinated leaves halfway across the map).
4. Simply use more apiaries, and breed bees with better pollination traits. That way you will generate pollinated leaves much faster.
