I don't think your feelings are misplaced, and please don't take what I was saying to mean that they ever were. A player's feelings are actually the most valuable feedback you can give us. This is a bit off-topic but hold with me for a moment.
We often see players generalize their feelings as "All/Majority/Most Players feelings X", but actually tends to work against the person's argument when really the most valuable thing for us as developers is what you the person taking the time to post feel. Don't make an argument on other players behalf, because you are going to be the best person to know how you feel about something.
There are some really great posts on this blog about this, the most valuable ways to give devs feedback, I read this daily and if you are interested in game dev I highly recommend them. So sharing how you feel about a change or feature is super valuable, even if it isn't the "actually X is very strong" we want the strong things to feel strong perceptions is often as/more valuable than the reality.
https://askagamedev.tumblr.com/post/149466049419/80-20-5
https://askagamedev.tumblr.com/post/157238832062/i-remember-your-52080-rule-and-it-was-an-awesome
Now to your actual question. Not every rune is going to appeal to every champion. Our hope is that each champion/class has 2-3 options that they can feel good about, looking at our data it does seem that this is largely the case, some better than others (the Domination rune slot is very...pick rate dominated by Brutal) whereas the Resolve slot is in a rather balanced state in terms of power and pick rate. Where as the Inspiration rune slot is somewhere in the middle, no single dominant rune, but people really overvalue Sweet Tooth given its power.
This is where feeling comes in, how something feels can often overshadow somethings actual power. A great example here is Grave's W (Smokescreen), for Graves this actually doesn't feel that great to hit because you don't really see the impact to your opponent. But as the opponent getting hit by Smokescreen can feel impactful (you lose all vision).
Minor runes are a big deal here, as they aren't intended to have a massive impact on your game, they do provide some bonus, but it shouldn't swing a game their own. This is why runes don't have visual effects (with the exceptions of Bone Plating). With these goals it kind of pushes runes to have a lot of invisible power.
You are right that there are situations where we give a larger bonus to melee champions over ranged ones, (Second Wind comes to mind here). Ideally we avoid this but it really comes down to the situation we are in. In Second Wind's case the goal of the rune is to survive poke/harassment in lane. Ranged champions have an easier time avoid poke, and are just generally safer than melee ones. Because of this we didn't want to give them the same tools as a melee champion, who doesn't have the same safety.
I'm not sure I follow what you are saying about AD/AP champions scaling with these runes. If you could explain that a bit more, that would be helpful.
Runes are intended as a way for you to customize your champion outside of the item system. Runes also tend to be more focused on the early game, where items take over more in the mid-late game. Though we do want some scaling rune options for players to opt into.