I've seen the same things you have. Memes that I think are really good go unnoticed. And questionable content reaches the front pages (although from your comment, I see you and I would disagree on what's questionable - I don't think it's right to hold memes to a standard of being original).
My best guess right now is that some of these anomalies happen because imgflip is still a relatively small community, and because most of the people don't check the Latest stream for memes. If there were more people upvoting and going through memes, some of the weirdness would be ironed out, but for right now, a lot depends on luck and timing (if you release a meme at a time when people aren't logged in and voting, it's going to get forgotten no matter how good it is).
But I'm sorry to say I don't have any special insight as to how the whole "system" works. I don't think anyone knows. I think people are fickle, and nobody really knows what people will upvote. There are certain users who seem to have an ability to make memes that connect with a lot of people, but most of those users say they don't really know what they're doing, either. And I definitely don't think it's based only on popularity. If that were the case, then all the memes of popular users would do well, and they don't.
What worked for me was making funny meme comments on front page memes. I started doing this because I realized nobody was seeing my memes, and I wanted to interact and make jokes where people could see them. People gave me positive feedback on it, so that's what I continue to do, and it's how I became well-known on imgflip, even though I didn't set out to do that.
And that's the advice that experienced users give to newer users on imgflip: be active and make funny comments on front page memes. The idea is that people will see your name and if they think your comments are funny, they'll associate you with funny material, and they may check out your profile to comment on and upvote your memes as well. But the truth is, that's only half the battle. Getting your name known might encourage people to visit your memes, but if they don't like a particular meme they're not going to upvote it. And so we're back to the fact that nobody can predict what people will find funny.
So I basically try to stay active with meme comments on front page memes, and make a variety of memes because I don't know what will work. Does any of that help?