There are scientific issues with evolution.
No. Not really.
Certainly there are some observations in evolution that have yet to be completely explained, but those are not issues with the observed fact of evolution itself. Over time groups of organisms modify into different, novel groups of organisms. This has been directly observed in controlled breeding in the short term (where millenia count as "short"), in embryology, in the fossil record over the long term, in genetic sequencing, and in so many other fields too numerous to list.
tl;dr: Evolution happens. Just like gravity happens. Deal with it.
There are a number of holes in the evidence that many scientists hope will be filled with future study.
Certainly there are gaps in the fossil record, but those don't disprove the observation that evolution happens. Claiming such would be like claiming gravity doesn't happen because you aren't watching apples fall from trees in Antarctica right now. Gaps in our observations of evolution are no more valid for making arguments against it than gaps in our observation of gravitation.
It would not be unfair to say that evolution has become the prevailing theory partly because science has yet to provide a viable alternative theory.
But evolution is not the prevailing theory. Because it's not a theory. It's an observation. Natural Selection, modified by punctuated equilibrium, gene transfer, gene drift, and so on, is the prevailing theory explaining the observed fact of evolution. And natural selection (modified by punctuated equilibrium etc.) is the prevailing theory because so far it is the absolute best, most tested, proven theory explaining evolution. In fact it is such a good theory for explaining evolution that people (including scientists who should know better) mistakenly conflate it with evolution itself.
Maybe finding a "middle ground" between evolution and creationism is counterproductive,
A middle ground between anything and creationism is counterproductive, because creationism is nonsense at best, charlatanry at worse, and demagoguery at all times.
but evolution as a concept isn't above scrutiny.
If by scrutiny you mean observation, then yes, because in science nothing is above observation (though for some things we still need to work out how to observe them). Observation is where science begins. Science then goes on to the tricky bit, which is explaining those observations, and then testing the explanations through experimentation and more observations. And this is where creationists and other people fuzzy on scientific reasoning get things wrong. They think that an explanation that gets invalidated or that needs to be modified somehow also invalidates the observations it inadequately explains. But it doesn't. Lamarck's theory of inheritance of acquired characteristics has been soundly disproven, but that doesn't change the fact that characteristics do change between generations. It only means that Lamarck didn't come up with a good explanation of how that happens.
It's a big problem that every challenge to evolution get filed under "creationist whack job work".
Because it pretty much is. Because again, challenging the observed phenomena of evolution is challenging the evidence of our own eyes. Literally mountains of such evidence. Meanwhile, challenges to natural selection happen all the time, some of which have led to a much greater understanding just how evolution happens (and the rest of the world, too - gene drift has some pretty far reaching ramifications), and have caused us to modify the theory of natural selection itself. So natural selection doesn't just explain evolution, it also has evolved as well.
How is anyone supposed to believe that a God would create dinosaurs, kill them, bury the bones under layers and layers of sedimentary shelves, each indicating a different time of progression and adaption?
Well, as a christorian, you should know that God is the biggest troll of all…
Meanwhile progression in human civilization is stemmied because of people like this. People that cling whole heartedly to the belief that some make believe figure is guiding their lives. Were you raped? They'll stand outside an abortion clinic and call you a murderer. Have a terrible incurable disease? Too fucking bad, deal with it, stem cell research hurts their imaginary man's feelings and you'll just have to pray you get better and regrow your organs back.
Probably the saddest thing about the creationists is their own childishly limited concept of God. They can't give Him any credit for subtlety. There's an old, sad joke about that which, badly paraphrased, goes something like this:
A Christian Scientist learns he has cancer. Being a good Christian Scientist, he doesn't go to the doctor, but instead prays to God for a cure. This works as well as can be expected, and soon enough he dies horribly and finds himself before God at the pearly gates of Heaven.
"What the hell?" asks God. "You're not supposed to be here for another 60 years."
"I thought the cancer was all part of Your Great Plan," says the Christian Scientist. "I prayed for a cure every day."
"But I gave you a cure, you stupid fool," replies God. "If I'd wanted you to die from cancer I wouldn't have put adriamycin in the dirt of that Italian castle."
Christianity, once the only salvation of knowledge for western civilization (IE; monasteries during the Dark Ages) is now the antithesis of everything we could be doing right in the world. Complete ass backwards loonies.
Actually that was mostly the Arabs, preserving the knowledge of the Greeks through the Persians. Most of what the European monks preserved was Roman drek. However, while a lot of the knowledge they preserved was largely useless, at the same time they were expanding knowledge all on their own through research and experimentation. Just look at Roger Bacon, Robert Grosseteste, Elmer of Malmsbury, and so on.
Even today the problem isn't Christianity. Not all Christians are loons, just some of them, so the problem isn't one of religion, or Christianity, but rather of willful (and enforced) ignorance. And I have to think that these people would be the same under any theology; their religion is their excuse, not the cause, for their bad behavior.
