The inherant problem with the rep system, as has been stated before, was that people farmed it.
As soon as it was re-introduced a little while ago, people would just farm it and within days be able to gloat at the sheer amount of rep they had, when they didn't deserve it.
Not only that, but often people would just rep up their friends, and forget about other people. Regardless of whether they deserved it (or they were even trying to farm it) or not.
In addition, i can imagine people who frequently posted in discussion got disproportional amounts of rep change.
If people disagreed with what the other person said, then their way of countering, without writing an argument would be to down-rep that person, who may just be expressing their view in a totally legit way.
Having said that, if it could be harnessed properly, then i think it could be quite cool.
For example, every time you gave someone rep you had to put a reason, and so it took a bit longer to give rep.
Also if the reason was 1 word or something, you could have some kind of mod reverse it.
Although i imagine that would be terribly time consuming.