These are my very simple suggestions, take them with a grain of salt.
1: Class Limit:
Limit of 2 of each class for BGs, eg: You can't have more then 2 rogues, 2 mages, 2 paladins, etc. I feel this has been needed for a long time. It is very frustrating to get put against a team that consists of 4 rogues, 3 mages, and 3 paladins. I know mentioning of classes if frowned upon, but there are tons of absurd "uncounterable" combinations. When you have a lot of one class, and the other team has a mixture of classes, the team with more of 1 class is usually a lot stronger simply because they can coordinate much easier, as well as having much more control of the battle. Is is never fun to run in with a healer and 2 other DPS classes, only to be absolutely destroyed by say 3 rogues, 3 mages, 3warriors, or 3 feral druids with their healer. It is the same amount of players, but be honest, who has the advantage?
2: Further map balancing / changes
We all know the issues with AV, and that Alliance has the advantage, as well as the Twin Peaks flag capture bug, Warsong bugs with the flag, many other issues that need to be ironed out. I am not aware of many bugs with the map, and I know it is very difficult for blizzard to make a completely balanced map, "perfection" so to speak, because no one is perfect. I just feel some of the maps need revisiting, as well as ironing out the bugs.
3: PvE items and PvP
I'll be blunt with this. PvP items you can obtain at the highest levels is very good gear, however there is imbalancing issues when people bring in Heroic tier PvE weapons, Heroic Item 2 piece set bonuses, or even Legendary weapons (see Staff, and rogue daggers, shadowmourne, Warglaives in BC). I commend the players dedication for gaining these items, which is very difficult, but the problem arised when Blizzard removed the "heroic pvp" gear IE: 2200+ higher item level items and changed them to simple recolors. The change/fix here is too either reinstate the heroic pvp items to counter the heroic pve items, or completely remove the ability to use heroic pve, or legendary items in PvP.
Edited by Feargx on 1/28/2012 11:10 PM PST