Well, I've completely removed squid from the equation, re-installed pfsense from the latest ISO and updated, then re-created the rules again. It still isn't working, and I'm just too frustrated to deal with it for a bit – it is making me feel really stupid, 'cause I just don't understand how the traffic is going where it shouldn't.
It isn't properly shaping traffic out or in for traffic that I've bound for specific ports, and checked 50 times to make sure that the traffic itself is behaving as it should. I've even rebound the rules to the wizard's default ports for the traffic I need to shape and it still isn't working.
I'll admit that much more traffic is indeed going to the correct queue without squid installed. But this was a non-issue with 1.2.3. So I'll wait for some stuff to happen.
The GUI needs some TLC. The wizard is broken, half the stuff in the configuration screens is not documented or explained -- which is understandable since nothing is set in stone yet and something might change that would require a lot of GUI rewriting. Rules that make sense in 1.2.3 are largely ineffectual in 2.x. I don't know if maybe the change of rule order in pf, or something else, is doing this.
Basically for me to test 2.x I'd need traffic shaping (and squid, my link sucks so I try to save bandwidth). Traffic shaping is too darn confusing to use right now, bad enough that I'm getting really niffed with it. So I'll sit back and wait till there is some focus on it in development, and I'll be happy to test it out for ease of use and functionality when it gets put into the spotlight. Right now it seems there are other areas that are more important.
But, I hope that it is looked at soon. QoS is important. I may not be a pf god, but I'm not quite an idiot. And if I can't figure out how to shape traffic that I know but the incoming and outgoing ports for, then there is something wrong somewhere.