There is much controversy on gravel vs. non-gravel lined ponds. I myself prefer gravel than bare bottom.
First, your not going to fill the bottom 1/3 of the volume with gravel. Are the rocks and gravel going to collect silt and debris over time, sure, but fish and other inhabitants will help stir the bed to keep it healthy and aerated. Just by walking around in the pond during maintenace is enough to stir it up and prevent dead spots.
Second, 1-3" of small (#6 and #8 washed in these parts) gravel provide a bed for BB, protects the liner from UV rays, and gives traction during maintenace. A little algae film on a liner is about the best slip-n-slide you could ever want.
Third, all the ponds I have built and maintain have rocks and gravel in them. Staying under 4" is the best thing. Once the gravel gets deeper than 4" you have to worry about anerobic activity. All the goldfish, albino channel, and snails burrowing in my pond keep the bed clean. Again, a little maintenance goes a long way too.
I am not saying gravel is the only way. I just would not do an EPDM liner in my climate w/o gravel. I have seen and loved many bare bottom Koi only ponds. With the right planning on filtration and other mechanicals, there are ponds that look great and the stock super healthy.
The choice is yours and what you prefer.