We use beacons, airports and VRPs because they are convenient.
When planning a route it is far easier to route between such identifiers, whether it be entering them in the GPS of dialing them up on the VOR.
Using other navigational marks would reduce the risk of collision at these choke points but it would be a pain.
It is however worth having a strategy for reducing the risk of collision.
Firstly, there is no need to fly over the navigational mark. Inevitably if you consider a typical route the beacons represent turning points at which you make some change in direction. Given that is what you are going to do, anticipate the change and simply cut the corner - you will be surprised if there is a significant change in direction how much you can cut the corner by.
Secondly fly up to the base of the TMA, that way the bu**ers can only get you from below or the same level.
Thirdly, always request a RIS.
Fourthly invest in a collision avoidance product.