Before 4.2, and after whatever patch last messed with my pet controls, I kept all my pets on defensive 99% of the time. As soon as I started attacking my pet would go in and attack that target and if I told my pet to go after a different target it would do so and then return to its original target. Perfect for PVE where you spend most of your time concentrating on a single target and occasionally focus on burning a secondary target/add down quickly. Most notably 4.2 took away the automatically attack my target when entering combat feature of the old defensive mode. Not a huge deal as I can just macro that feature back into all my shots with something like the following.
I've yet to try it as I've only done the Thrall chain and one ZG run on my hunter since the patch. One perk of wiping repeatedly on the last boss in ZG was that I got a lot of practice playing with the new pet stances with all those adds. Assist mode was pretty much useless and I felt my pet spent more time running around than actually hitting anything. Not to mention that when assisting it was near to impossible to get my pet back to pull a new add off of me. Defensive mode was best, but I had to pay a lot more attention to managing my pet's target.
I used to use aggressive for waves of mobs and/or PVP when I really didn't care what my pet hit so long as it did it quickly. I haven't PVPed on my hunter for the longest time, but I fondly remember standing back to back with my pet on aggressive to provide 360 degrees of stealth detection. In other words I won't miss it too much, but still assist mode is certainly no replacement for what aggressive stance provided.
One thing I like about assist mode is that it feels a little more like a pet command than the other stances. What I would like to see replace/augment the pet stances are three commands: assist, defend and heel. Assist would behave much like assist does today with the exception that if I specifically command my pet to attack something else it will do that instead and then go back to assisting. Defend would focus on defending me and turn my pet into a pseudo tank focusing on and switching to targets that are attacking me first (to pull them off). Finally the heel command would call your pet back to your side where it would remain until instructed otherwise (basically a rename of what passive does already).
To extend that one step further the assist and defend commands could be used on another friendly target! How cool would it be to ask your pet to go defend your healer, or in a raid/dungeon setting have your pet assist one of the melee DPS or tank. It would totally turn what is still a little bit of a kludgy interface and make it feel like our pets are actually listening to our commands and working alongside us. The immersion factor alone would be enough to make me squeal in delight.
I can only hope that the developers working on the pet changes are thinking something along those lines for a long term plan. Short term the new pet changes are pretty disappointing. Assist mode has your pet actually fighting against your commands at times and defensive mode requires more attention that it did before. New players are going to have a harder time controlling their pets than they did in the past, although they don't have the aggressive mistake to make anymore. I just picture new hunters trying to use the assist mode, getting an add on them while killing another and getting totally frustrated trying to tell their pet to help them get it off.
Oh and while I am listing totally awesome pet enhancements I'd also like to suggest a new commands similar to "go to" called "patrol". Your pet would walk back and forth patrolling between their current location and the location you selected. Basically a carbon copy of a feature that existed in the first three warcraft RTS games. I'm not sure how useful it would be in practice, but it would be fun.