Some characters still take the war in Azeroth seriously, and kill everyone of the enemy faction they can. They did this before the patch, and they will continue to do it.
There are reasons to engage the enemy now, which were sorely lacking prior to 1.4. Unfortunately, these reasons aren't really a big improvement to the PvP system. Having a counter for Honorable Kills is nice, but it has no impact on the game world. Contribution Points give you something to strive for, but again, their significance doesn't extend beyond better gear for a handful of players. Subsequently, PvP battles remain as indecisive as they always have been in WoW.
For example, here's a common PvP scenario in the game. Several players call for help because they have encountered higher level enemy players in the area. Their faction heeds the call, and reinforcements arrive. After overpowering the enemy with numbers, a brief sense of victory is shared, but this vanishes when a few minutes or seconds later, the same group of enemy players is staging another attack in the same area. In order to protect lower level characters you must essentially stand watch over them, which can get boring pretty quickly.
Another serious concern is that no effort has been made to balance Alliance and Horde populations, and Blizzard does not disclose these numbers. There is little doubt, however, that the Horde is substantially outnumbered on at least a few servers, putting them in a more difficult situation than their opponents.
Death Without Consequences
This brings to the forefront several problems with PvP in WoW which I've mentioned before. The consequences of death are, at the most, trivial. The nearest graveyard could be anywhere from a few seconds to a few minutes away. If you choose to recover your corpse, there are no equipment durability penalties, so about the worst thing that can happen is that you have to wait a little while for a safe opportunity to revive yourself. When you come back to life you are low on health, so it's wise to take some care. Nevertheless, if you're within a minute of the graveyard, it makes little difference how many times you die.
Such it is that raids on enemy territory typically go on until one side loses interest and decides to leave. Even if a large enemy raid is scattered by friendly forces, it is only a matter of minutes before corpses have been recovered, characters have been healed, and the raid is regrouping nearby for another round. Not all players object to this, but it does make PvP pretty hollow.
The obvious solution would be to introduce some way to control territory, or at least lay claim to a graveyard. Blizzard has entertained this idea, but it certainly won't come about until Battlegrounds, the next big content addition to the game, have been implemented.
Tarren Mill Under Siege
One unusual thing about WoW is that the two opposing factions have no common language. You can't send private messages to the enemy, and all local chat seen by the opposite faction is garbled, so you can't see what the enemy is saying. The only cross-factional communication that seems to work is emotes (and, as you may have guessed, this has led to petitions to have the /spit command removed from the game).
Being without communication, there are a limited number of ways to find out what's going on in the world at large. Other than the system messages that appear in the world defense channel when a friendly town is under attack, the only way to stay on top of enemy activity is by networking extensively with your own faction. The point is that if the two sides want to meet somewhere for a big battle, there is currently no mechanism in the game to arrange this. Subsequently, certain towns, such as Tarren Mill, have become the front line by default. They are now the place to go for PvP, and the battle rages on almost 24/7.
Caught in the Lag
Broadband Internet has gone a long way toward minimizing lag in online games with small numbers of players, but in MMORPGs it remains a way of life. Extremely large battles involving hundreds of players are just inherently slow because of all the data that has go to and from every character in the fray. While having a lot of RAM in your system does help to alleviate the problem, there are no affordable ways to completely eliminate lag. Many games limit the number of players in a given area for this very reason. That said, WoW handles large raids better than most games of this kind. I'd guess this is partly due to the lack of collision detection (players can pass right through each other).
I don't think the honor system has affected gameplay nearly as much as the WoW forums might lead you to believe, or that there will be any mass exodus of subscribers as a result of it. Although it is a small step, it is a step in the right direction. Hopefully upcoming additions to the game, such as the promised PvP Battlegrounds, will further improve the game's lackluster PvP system.