Let's look at the three questions and evaluate what they are asking for.
- What things should an indie game developer never do?
This is asking for a generalized list of stuff that game developers are encouraged not to do. And that's why it's not acceptable.
The fundamental purpose of all Stack Exchange sites is to build a functioning, searchable knowledge base of useful information, such that people can later find that information with ease (typically from a real search engine like Google). A list of suggestions for game developers to avoid is not searchable; it's just a random list of stuff. If someone found this question, it would only be by actually searching for "things not to do".
And people don't search for that stuff.
It's not even a comprehensive list, so if you're looking for things not to do, you haven't actually found it. You've found some things, but not all of them.
It's also too "chatty" of a question. While people could post their personal experiences with things they've done or seen done, people are more likely to just come up with stuff off the top of their heads. And the stuff will have no rhyme or reason to it: some will be game design, some will be programing, some will be art, etc.
- How to prevent the "Too awesome to use" syndrome?
Is this question opinion-based? To a degree, yes. But the question is very clear and specific about what it's talking about trying to prevent. This invites people to provide theories of why this syndrome happens and therefore how to avoid it.
People are being invited to provide opinions on how to solve the problem. But that's not very different than people posting opinions about how to fix a particular program. People have different ways of solving the same problem. The thing that makes this question good is that the question itself is reasonably stated and meaningfully scoped. And thus we can judge answers based on that.
- Are boss battles important?
This is really just a bad title. The question could be improved to ask about what bosses are and what function they serve in a game. And again, while it does invite opinion, it's still a specific, meaningfully scoped question.
On a site where less concrete, more subjective questions are allowed, we have to use good judgement to determine which ones are worthwhile and which are not.
Apart from closing them is there anything else we can do to prevent debate, arguments, polling, or extended discussion? Is it possible to deal with primarily opinion based question in other way?
Like what? It's a binary choice: we either shut them down or we allow them. Anything less than switching them off is tacitly approving of them, thus encouraging others to provide the same.