In order to show why I'd like this functionality built-in, I'll give you a real example from one of the forums I administer.
1. In order to promote activity in certain sections:
We have a Reviews and Library section as well as a section where items can be given away. These sections are moderated and have a very high standard for posting, and require sometimes 1hour+ worth of work in order to be approved. Back when we were running Vbulletin, these sections were swarming with activity. Why? Because we offered a reputation point from staff for every approved thread. Since 2011 when we moved to XF, one of these sections has had a total of 4 new threads. This is a section which as a total of 953 threads. Without an incentive to post in the form of Rep, we've essentially killed these sections.
2. In order to promote excellent posts:
This is somewhat the same as the above mentioned point, except that it promotes above-and-beyond posting throughout the entire board. Especially in our case, the News and Politics section. People would go to extreme lengths to make amazing posts on current events, politics, etc., because they knew they're much more likely to garner rep points for such posts. The likes or the Advanced Ratings add-on works fine to promote activity, but not to promote a high standard of activity like the reputation system.
3. In order to provide a method of oversight:
Unlike the likes or advanced ratings add-on, reputation can be monitored, can restrict users from repping their friends too much, and can require stated reasons for why the rep was given which are publicly listed on user profiles. This provides a level of oversight in order to keep reputation fair.
4. In order to provide a longevity to the system:
Without a native rep system, there is no way to provide longevity to the system. We have experimented with substituting the functionality with add-ons, but have found they are regularly unavailable for new versions of XF, they lack functionality and fixes, developers discontinue support over time, and current reputations are unable to be imported from one system to the next. This is a glaring problem with boards such as ours when reputation is earned with such hard work, only to wiped away with one update. It essentially locks us to old versions of XF.
XF is not vB and I recognize the need to differentiate XF from other forum software systems, however, for us (and I'm sure for others), the lack of a native reputation system is a glaring lack of functionality that leaves us in a tough situation. On the one hand I love the XF system, but if the next generation of XF means utilizing a system that lacks a functionality that we quite desperately need, we'll have to move to another platform. Something we really don't want to have to do.
I recognize that some of these problems can be overcome with other solutions, however, none as simple and as effectively as with a proper reputation system.
Finally, I would respectfully request that if you don't want a reputation system for your board to keep that to yourself. If the developers include a rep system, you're not forced to use it. I'm not asking to remove the likes or any other functionality, just to include some options for people like us that desperately need it.