You seem against systems that measure time instead of skill, but the whole honor-marks system measures time instead of skill. The old peak-system *also* measured time instead of skill but measured how much time you spent in a single week instead of cumulatively.
I am not necessarily against systems that measure time. For example, Reputation is a very good system for rewarding time spent. What I am against is reward systems which encourage "incorrect" behavior.
If time is the behavior you want to reward, then reward time. But in Battlegrounds we don't want to reward time, we want to reward people participating in PvP. The hard part is defining participation in PvP. In particular, it's very hard to tell if a person is defending a vital node, or is merely slacking. It's very easy to over-reward attacking, which leads to all offense, no defense games.
So we use time as a proxy metric for participation. But it's not a perfect match, and the AFK'ers exploit the difference between time and participation.
Imagine if AV had zero rewards. No honor, no reputation rewards. How would people play? Most people who actually bothered to go to AV would go there to win. There would be no point to being afk (unless you're a weird passive-aggressive griefer). People who need to go afk because of real-life concerns, would still go afk.
People only go AFK in AV because of the way the reward system is structured. Multiple quick losses can be worth more than a drawn-out win. You don't lose anything for indulging in negative behavior.
Secondly, when it comes to PvP, I believe that rewards should bias to the skilled. I think the Arena system is a fairly well done system (with the exception of being able to "sell" high-ranked teams). It rewards the highly skilled, but is still attractive to the less skilled.
Arena rewards victory, and time spent. But the reward for time spent is not linear, you don't get more arena points if you put in more games. You just need to do a minimum amount of time, and then victories determine the scale of your reward.