After reading this thread, here are my following suggestions.
Fix Pet AI.
Follow should be follow. Period. If something is next to the pet, fine, it can hit back, but it should keep following the owner. And the proper follow, not the pathetic way they do now.
Kill should be kill. I sick my pets on something, their focus should be 100% on that target untill it's dead, or cannot be reached.
Guard/auto defense. This ones so messed up it isn't funny. Why does my pet hug a wall when a mob targets it from 3 rooms away? If there's no LOS, there should be -no- response.
Pet Ball Charges according to Follower Slots.
SHORT Cooldown, 10-30 seconds.
Combined with a increased charge usage (AND the trans powder quest change) this should severly limit the ability to chain summon a pet. I personally think the cost alone would limit it.
Auto Stables changed.
How often do pets check for their masters? 5 min divided by how ever long that is, failed checks results in the animal going to the pound. They cannot be summoned, they have to be collected. (Also removes them from follower slots)
This should operate all the time, at any time, wether the owner is logged in or not. I know this would affect several aspects, including leaving Cu's in a spawn area, and people leaving packys at dungeon enterances (negative really, maybe this shouldn't apply to pack animals, but auto stable doesn't already so maybe it's fine)
Animal form, sorry, but these should count as follower slots. They should -not- be able to be used as a way to bypass control slots. Everyone else needs to deal with it, Ninjas should not be exempt, for the negatives of animal form, there are positives, bonus's, mount on the run, etc.
Pet Commands. Whisper should work like it does for people. I love using whisper to command my pet from a screen away, but it doesn't make sense.
Couple Side Notes;
I would have no issues if pets were nerfed, as long as we were able to equip them, or feed em statscrolls, or other forms of customization.
Pet Training should be looked at. Either increased speed at training, or the removal of stat loss on death. They -are- a pain to train, especially things like magery, and loosing .1 could take -days- to replace.
Got no issues training pets, but with skills lost on death, it needs to be tweaked.