I think they were trying to stop the abusers with a technical solution instead of a policing solution. Truebox was probably more a Public Relations counter to the armies of bots people complained about on Ragefire (which by the time the first Truebox had come out had earned the nickname Magefire). Regardless of the way that people were running those bots, it was bad PR and gave a perception that DBG couldn't control cheaters on their servers.
Truebox was a PR salvo of "limit without policing." It worked to shift the view that DBG cared about stopping abusers, but the people who are going to abuse MQ2 to the detriment of other players are going to use whatever edge they can get, so they did and they moved on to other methods. This is where things like AoCs (implemented at the same time as Truebox) served to make abusers less visible.
If you go back and look at posts from each Truebox server, you'll see that people abused cheat methods to the detriment of other players on whatever they could -- Efreeti, Runnyeye, VP Keys, Howling Stones Keys, Storms Minis, etc. DBG solved many of those problems by changing those specific mechanics. While AoCs (and of course, their predecessor, picks) served to reduce some of that -- abusers abuse.
Unfortunately for MQ2ers, it doesn't matter WHAT software someone is using (or if they're using a hardware solution or poop socking it with 50 computers) the PERCEPTION from players unfamiliar with MQ2 when they get trained/forced out of their camp/KS'd by a multiboxer is that it was someone using MQ2. You can corroborate this by looking how many times people are so sure that MQ2 is being used on Truebox even though we know mule doesn't support that. The perception from the impacted players unfamiliar with MQ2 is when someone cheats to their detriment -- it's MQ2. (Sometimes even when it's not cheating, just a good boxer). Again, unfortunate for MQ2 users.
So I suspect the litany of changes are cumulative and the idea of Truebox continues to combat the idea that DBG just doesn't care about cheaters. There are players that stance matters to and their voicing of the opinion that EQ is overrun by bots has a heavy impact in the PR realm. When really they're just talking about people who use third party software to the point of abuse. Which, I think the majority here don't want to abuse to the detriment other players. Still, perception is perception.
I too had hoped they would implement a box server with AoCs because I want to use MQ2 in a place where I won't impact other players. I don't want to build a box army to fight the people who lock down spawns using third party software (even though I am quite capable). But I suspect they're worried a bit about the PR backlash from people who will see a non Truebox server as an OK on abuse versus just a place for boxers. Hopefully DBG will realize that they could try anyway and see what happens. That they released two servers at the same time had me hopeful.
At any rate, my primary want is AoCs on a MQ2 allowed server. Everything else is secondary. I play either way and eventually that sorts itself out as AoC servers catch up to live. Still, I wanted it now~