I'm tired of hearing that "using the directed axis mate is bad because it over-constrains your assembly", or, "NOT using the directed axis mate is bad because then your assembly is UNDER-constrained".
Neither of these is necessarily true. It completely depends on the situation.
Here is an example of a situation where the directed axis mate is necessary to fully constrain the assembly, but it does not over-constrain it:

In this case, a directed axis constraint is necessary to get the horizontal leg of the elbow aligned with the ball valve AND facing the correct direction. (That is, just as necessary as having mate/flush direction control is... yes, I could use an undirected axis mate with an Angle constraint, but how would you like for all face-to-face constraints to be undirected and have to apply an extra Angle constraint for every single one?) The directed axis mate is just the right tool for this job.
And here is an example where using the directed axis mate is NOT necessary to fully constrain the assembly, and in fact using it would over-constrain it:
(Sorry, the system won't let me embed the Screencast, so you'll have to click this link to watch it: Importance of a free-direction Axis mate)
In this scenario, the mate/flush constraint controls not just the position of the pin but also its direction, so enforcing the direction with the axis mate as well would over-constrain the assembly, and result in a sick assembly if the flush constraint changes direction, as shown in the video. And this is why Undirected was left as an available solution.
So, does using a directed axis mate automatically mean an assembly is over-constrained? No. (i.e. the second example). But is it sometimes necessary to get a fully-constrained assembly? Yes. (i.e. the first example).
The fact that the directed solutions were added, or that the undirected solution still exists -- neither of these facts is an issue. Please stop complaining that "directed" was added or "undirected" still exists. Both of these are tools, and are very useful in the right situations. If you don't need one of them, don't use it.
The only issue here is the default behavior (the fact that a directed solution is enforced automatically when creating a new axis-to-axis constraint), and that's the only thing anyone should be complaining about.