First thing, I have to say right off that none of these things are under our power to change. The software is designed that way, and RPG.se doesn't have control over the software. I will attempt to explain why they work the way they do, though.
So there will be no answer that is put into use, because RPG.se can't change the things you've brought up. (The place to propose change to SE network software is Meta.StackExchange.com, but as will become clear, these three things aren't up for negotiation anyway.)
Reputation is functioning as intended
The reputation system is a gatekeeper: only users who have learned how to contribute to the main purpose of the site earn access to things that are not the main purpose of the site. Anyone can ask questions and post answers, even anonymous users. Users have to figure out how to do those two things according to RPG.se's goals before they get access to any other abilities, and that's very deliberate. The Stack Exchange model strongly emphasises asking and answering questions, so only users who have figured out how to do that in the way SE needs can unlock more privileges.
Held questions are functioning as intended
The point of a question being on hold is to prevent answers. That's 100% the point of it. There will never be an option to answer questions that are on hold.
Holding (and closing) questions exists because Stack Exchange specialises in only certain kinds of questions. Any question that is looking for discussion or opinions is off topic, because the point of Stack Exchange is to handle questions that have solutions, not discussion or argument. SE was invented to do what discussion forums do poorly (solve problems), and will never be altered to try to handle what discussion forums already do very well already (general discussion, brainstorming, and opinion sharing). When people submit questions that don't fit they get put on hold permanently.
The question you mention, https://rpg.stackexchange.com/questions/66908/5e-striker-what-class-should-i-be, is on hold because it's asking for ideas. It will stay held, and in four more days it will graduate to [closed] instead of [on hold].
However, it will remain votable. The purpose of votes is to sort questions, and held questions still need sorting. Votes give or take away reputation for the post owner, because that's part of the point of the reputation system: useful questions are rewarded with positive reputation, and the kinds of questions that RPG.se doesn't want people to ask more of are rewarded with negative reputation.
General shin kicking either gets better or worse, depending on the user's choices
The shin kicking isn't actually kicking. It's more like someone walking into a thorny bush and suffering the scratches that naturally causes. Getting ripped by thorn bushes stops happening when users notice there are signs marking the path, and stop walking off the path into the thorn bushes. The thorn bushes exist to protect the sensitive parts of the site, which if walked on, would eventually destroy the site's usefulness and reason for existence.
New users generally don't already know that walking over there causes damage. Also, because most other places on the internet let people walk there, new users here often assume they can walk there here too. We have a tour and help centre that says “don't walk over there, please stay on the paths, thank you,” but there are always 10 people who don't read that for every one who does, and of those who do read them, full understanding of their implications is rarely automatic. The negative reinforcement of the reputation system is to enforce the rules and protect the site, whether people have read the rules or not, and in general to teach the practical application of the rules.
A new user who keeps on running into the negative reputation effects (walking into the thorn bushes) is causing a problem for the site: they're not following the rules or purpose of the site. Rather than suffer the problem though, the site makes that user responsible for solving the problem: it lets the user decide when they've had enough thorns. When a user decides they've had enough thorns, they do one of two things:
The site is okay with this, because what the site is doing is very specific and is not what everyone is looking for. If someone personally doesn't work well with both negative and positive feedback, they won't like it here and leaving is the right choice. Similarly, if someone has mistaken RPG.se for a discussion site, they should go elsewhere, because discussion sites are elsewhere.
The site is okay with this too. A user to adjusts how they use the site until they start getting positive feedback has started using the site for what it was designed for. That's an improvement in the site's goals and purpose.
It's like learning to skateboard: when you fall it hurts, and when something hurts you learn to stop doing it. To stop falling, you either by giving up learning to skateboard entirely, or get better enough at skateboarding so you don't fall very often anymore.
The held status and reputation system are functioning exactly as intended. They worked to make you do something different: post here! You decided to adjust a little bit, instead of leaving.
That means that you have another chance of learning how the site works and what it expects from users. You also know more now that RPG.se isn't designed to make everyone happy or be used for everything related to RPGs; it's designed to attract people who want to work with its system, and be unattractive to those who aren't interested in doing what it aims to do. It's not the only place for RPG stuff online and purposefully doesn't try to be.
Now you have some context for understanding why holds, negative reputation, and a bumpy ride for new users exist, and if those goals sound worthy to you, you'll adjust a bit more to accept them as a necessary evil outweighed by the good they do. If not, you might be closer to deciding that what RPG.se really is about isn't what you were actually looking for, now that you know a bit more about what RPG.se is for. Either way, the site moves that tiny bit closer to being in harmony with its purpose and the users who help it get there.