Nearly all beginning writers worry about "long term weaknesses." And nearly all beginning writers have a reason to worry. I was the same way twenty-some years ago. I didn't even know what my weaknesses were, just had a general lack of confidence. I got the help I needed by joining a writers group dedicated to the goal of having everyone's work published. There were 2 English Lit profs in that group and we had many aspiring writers show up and drop out. Believe me, they tore my writing to pieces. Then I would go home and rewrite for the next meeting. I stuck with it for several years before submitting to major magazines and being rejected. A few editors at small (but paying) magazines began accepting poems and stories and I even got fan email. It never would have happened without the help I got from the group.
I concentrate on novels, now, but still haven't got an agent (had one once, but she was lousy) or major publishing offers. I prefer to think it's because I don't write genre novels that agents might see as potential sales winners, but maybe my writing isn't up to par, although I've gotten so many compliments over the years that I don't think I'm a lousy writer.
As for your question, it's all about "suspension of disbelief" on the reader's part. It's not that hard to get in the overall sense, because humans have a remarkable capability of imagining dragons, orcs, faster-than-light travel, magic, etc. They can also accept impossible characters such as Superman, zombies, etc.
But when it gets down to details, you can lose the readers. Your characters must stay true to character and must have motivations behind their actions. You can't have a cowboy character and give him a New York accent.There are dozens of other mistakes a beginner can make. I suggest you google "Turkey City Lexicon" and see the list of newbie habits that a writers group once drew up. But most of all, I suggest you get input from other writers. Posting your work on forums for critique is okay, but you'll mostly hear from beginners like yourself. My pet peeve is the ones who answer a serious writing question, beginning with
"I'm not a writer and I have no experience with your question, but my opinion is. . ." or "Yes, I have the same problem," without offering suggestions. If you begin taking note of those reponses, you'll soon see how many newbies are on writing forums just to "chat."
Find a writers group in your area or online and get critique from other writers. Also, critique other writers and you'll see mistakes you want to avoid. Asking questions about technique when no one has seen a sample of your writing will get you nowhere.
Hope that helps,