Oh, you also mention characters acting oddly to make the story progress, but this is fairly common in plot-focused VNs. In early VNs, it was mostly because of the philosophy of 'gotsugoushugi', which is a game-maker philosophy for plot-focused games with multiple routes where character actions and even personalities are warped at a moment's notice solely to move the story forward. The real issue is a matter of degree. For instance, there are a number of VNs I can think of off the top of my head where the personality change of a main character was so dramatic it completely broke me out of my engrossment in the story. The most egregious example of this I can name right here and now is Tsuki ni Yorisou Otome no Sahou 2. During the common route of the game, the protagonist is an arrogant, immensely capable person with a wide variety of talents, but in each of the heroine routes, his personality gets toned down, his talents weakened, and his motivations twisted in ways that don't make sense even in the context of the route. This is an example of going too far with that kind of tactic.
More subtle are the random bad endings that pop up in a lot of horror and action VNs (especially early ones) where the actual choices result in random horrible deaths that make absolutely no sense in the chronology of the story. These games were the reason I started resulting to using walkthroughs for all VNs, because I got tired of making choices, only to end up with senseless bad ends or normal just friends endings. However, at the same time, this degree of manipulation can actually result in a positive result, as while those endings were often frustrating, they were also part of the experience as a whole and made it richer in some way.
To be honest, it is one of those JVN storytelling techniques that can be either excellent or horrible depending on how well it is utilized.