Opus,
If the choices were automatic and rule based we would not need gate agents for these decisions - software and systems can take care of it. My answer (if we were gate agents) would be: No right answer for all occasions. Depending on the circumstances every answer is correct. As a gate agent I would use my judgement within the broad policies of my company and its customer needs. I need computers as tools to give me info to make the choices and let me know of specific entitlements (a voluntary downgrade who should be upgraded, etc.)
Let us start with the first scenario. What if my airline screwed up and I had this particular pax on a non-upgradable fare (RTW) who has travelled already for 18 hrs and has been delayed because of the error by another gate agent, airline procedure, etc. I would upgrade him first (especially if he is an elite pax).
Also, what if I had a lot of open seats and our "general policy" is to deny upgrades most of the upgrade candidates (either because of the fare basis or some other restrictions). Shoud I consider the "open" nature of my biz section, to allow some exceptions or stick to the rule. Mind you by "doling out" upgrades that pax are not entitled to, I may "dilute" the product (biz experience). It is judgement call.
If I have my company's best interests at heart AND feel empowered and feel supported by my mgmt I would risk decisions and not always play safe. I know that rules are there for the norm and when I trust my experience and judgement in spotting the exceptions (empty biz class), I will make the not so easy decisions (allocating upgrades to select sub-group and not all). It may actually be the Honeymooning couple in your example 2 (in addition to those entitled). These couple may be loyal to my airlines for the rest of their lives.
I sympathize with the core point you make - sometimes elites act as crybabies and there is arbitrariness in expectations and gate agent behaviour. However, I do think, that is the nature of the beast. There has to be room for variance, gate agent flexbility, elite expectations. If there is no charm of surprise, some of the intangible benefits of FF programs is lost. It cannot be common sense always