Oooh :) I really like the item slots that you've cooked up. Vury nice.

I'm not sure that pets should be marginalized as +2 flanking buddies. It seems a complete waste of a thematically important game mechanic. This isn't something that you've caused of course :P I'm railing mostly against the fact that you are correct, the rules for pets are ill-thought.

And so if there was ever a need to adjust animal companions, it would be in the later levels when their damage means little to nothing, when their survivability is slim to none, when combat maneuvers are benched due to either immunity-from-shape or immense size.

I hope this is a helpful evaluation of your table above :) As the nerfed level adjustment makes them less imba at the early levels, which is a good thing. But in the later half of the level tree, they're worse off than stock rules would allow. Which, again, by stock rules animal companions are already useless, now they are more so.

I've really enjoyed discussing this with you, and would like to make a general suggestion: Have pets level by your rules or stock rules from 1-10, then introduce Pet Prestige Classes to address the flaws and inadequacies in their mechanics in the later levels. I would enjoy seeing some of your ideas :)