It could be like just how the old mechanism worked or a few improvements can be made too,
Answers :
1. Just like how it used to work before, yields are set on a random basis and fame is produced over time ( Subjected to improvements )
2. Capturing would be like before, taking over the site will mean that it is now the attacker's site and it can be attacked again by other clans instantly, but ur concern was for the prolonged wars that benefit none, for this, and to replace Supply Charges, we could have a fixed cost of DD required to attack a site and sites that have upgradeable hp that requires DD for upgrading or a system where the DD cost of attacking a site is variable, for example, more recently taken over sites could have a higher DD cost for attacking and in due time, the cost reduces till preferrably zero over time. So, we could have sites producing fame items over the time held by the site owners. ( Subjected to improvements )
3. The answer to this question is included in the 2nd point.
The reason I bring this to discussion is because, every server seems to have a different scenario, like in EU2, there is almost no fighting ig, and in Asia, its pretty stable but players arent in big numbers and it changes ( I'm in Asia ), people here only swap gates. So, by introducing this mechanism, we could provide players varied gameplay according to their situation or by time. And to reply to ur last paragraph, I dont stay awake till early morning to steal gates but it is not wrong for them to think that way too. Because, a fun part of the old site mechanism was that, there could be ambushes, sudden drains, sudden bullying, etc. you could attack or get attacked anytime, that could be a pro as well as a con, it had more freedom. So, looking at all this, we can arrive at better solutions. The fixed phases have their own pros and cons. And yes, an individual or a small group of players could find it hard to find benefit from fighting big alliances but even before these updates and gold ores, an individual player from my server was able to win governor from just daily fame. The ores are also helpful, so people can also farm that in both mechanisms.