The long and the short answer is that the ego often searches for ownership and depends upon time to do its work.
The matrix represents the past. The real world (as expressed in the movies and animae) is the future. Within the matrix, the past, you have different forces vying for ownership of our mental forces. As we become more conscious of the past (the matrix), these forces try to bend us to their will. The machines find solace in the mystical world of numbers. Zionists fight for the future, but they are not exactly privy to all its machinations. Mervs are the owners of the past's past.
This is how things sit and even though all these creatures may be conscious of the future world's problems. None are willing to deal with it in the present except for Neo. And, this is his great accomplishment.
Morpheus, being a part of Neo's ascension, wants that back. He thinks that if he owned the body, the spirit will come with it. He showed us Neo's spirit but could not capture it. In other words, he's thinking at a carnal level and who better to take him out than the one who understands carnality better than anyone else, The Merv. To keep the Merv in check, Zion takes on the threat to the future, in this case, the Assassin.
The storyline then follows how different people will try to own whatever is perceived to be important to them. Some will treasure the past, the Kid with Neo; Niobe with Morpheus. Some will focus on the future, the General wants to own the world, Cryptos wants the redpills quieted. But, all will not deal with the present as the present and because of this they are stuck in the egoic mind state that makes it so easy to destroy others.
We deal with the present. We are the ones who determine what happens in the matrix by shaping in the present (even though it really is the past). In this game, we have no choice but to be in the present. The idea of the game is to shape it and this is what makes the LEs (Live Events), randomization, and interactivity so important. IMO, interactivity (beyond combat) is the most important.
If you're wondering why this is a RPG, it is so because of the choices you make along the way. Your development is greatly weighed by the strategy you take. This game is 98% soloable (if that is a word). Despite this, most people jump into a faction right away. They fall to victim to "group think". Funny thing is three lines of typical thinking (strategies) result from this. 1. Cheat and exploit the game (a growing segment). 2. Don't fight at all (for those who insist that this game is wholely social) 3. Don't cheat (which is becoming the minority). Without the devs doing a thing, we already have three ways of handling the present. Are they functional? Mostly, yes. When certain groups leave the game (exploiters generally leave after the exploit is fixed), the consciousness of those who stay will begin to grow. Then, you'll see the game grow as a whole.
Well, anyway. Enjoy 