So, what's the solution? It's multifaceted, but it's not complicated. As a first step, I think Indie authors need to cultivate critical readers and listen to their feedback. When you find such gems, don't give them the book until you are certain it's ready to publish. Ask for comments on the story structure, the ease of reading, and the pacing. Try to get the reader to zero in on specific examples to illustrate any criticism, but don't expect that they will point to the precise problem. These folks are hard to find, but they're there. If you're depending on a relative, be sure to explain that the purpose of their feedback is to keep you from embarrassing yourself in public, not to make you feel good right now. Although my wife is fond of me and likes to say nice things to me, she won't let me go out on the town with my shirt on inside out. I've tried it. There are some others who help me, as well, and when some or all of them tell me that there's something wrong, I know there's something wrong. They may all point at different things, but that doesn't matter. It's my job to find the specific problems and fix them.
As a second step, if grammar and punctuation get in the way of the story, the writer (or editor, in some cases) needs to go back to school or find a different outlet for creative urges. An editor should be correcting oversights and mistakes, not picking through the fruits of ignorance. There is a difference between an editor and a ghost writer. Let's not confuse the two.
The third step, and the one that all of us who are serious about removing the stigma attached to Indie authors should embrace, is to give honest, direct feedback, as opposed to "I'll scratch your back if you'll scratch mine" reviews. That's best done with some degree of privacy, as opposed to posting a critique for the world to see. If you read a lot of Indie books, as I do, you've encountered some that have egregious errors in the first few pages. Take a minute to write to the author and suggest that, while the story might be interesting, it's obscured by the poor grammar and punctuation. Don't give it 3, 4, or 5 stars and hope for the same in return. That's where the stigma comes from.
Is there a place for paid editors, cover designers, and blurb writers in this world? Certainly, there is. The good ones earn their money, as do good writers, and their work stands out for the same reasons. Let's all focus on the quality of our collective product, and the stigma will go away.