I have brought interesting delimmas with evidence being either inexplicable or contrary to evolutionary doctrine. Others and myself who seek a more strongly supported theory within science are ridiculed and thrown into the creationist category.
That's unfortunate. Do you really bring empirically evidence that hasn't been accounted for previously? I only ask because the other evolution critiques here have only peddled dead criticisms, either honestly mistaken or with the intention of pulling a fast one over the unaware. If you do have empirical evidence that clearly contradicts evolutionary theory, then I'd like to hear it.
It should be a fact that is already accepted and not simply an unanswered question (e.g. I don't see how x could have happened, therefore it didn't). Also check if www.talkorigins.org hasn't already discussed your objection. If they have then argue why the response is inconsistent with scientific knowledge (In contrast to "If we take it down to its root, it rests upon a philosophy that makes me uncomfortable." Everything in science from evolution to automechanics to forensics can be boiled down to naturalistic philosophy if you really think about it).
There are some "faults" if you want to call them that in current theory that need not be distorted by those terrible Christians.
They are certainly questions that specialists are debating in academic circles. Unfortunately, creationists and their disguised cousins, intelligent design theorists, choose not to engage them before an audience of informed scientists. Instead, they proclaim their ideas in church debates, videos, and media stunts. Their goal is not to improve science, but rather to win converts.
There are scientific alternatives to the black and white of Evolutionist (science) vs. Creationist (religion). I find that many scientists just don't want to hear it.
Perhaps your predecessors have made such a bad name for themselves that it will be harder for you. If you are persistent and and actually have good evidence, (i.e. you're studying and discovering the stuff yourself and not getting it from a hack) then eventually the scientific community will listen. If you turn out to be right, you'll have a Nobel Prize coming for sure.
In response to your last statement, I find myself asking whether Darwin's evolution is testable or falsifiable.
It certainly is. I think some critics today get frustrated when a question like "How could the human eye have evolved?" fails to make biologists recant. Unfortunately for those who feel uncomfortable with the theory, it has done such a good job of accounting for evidence from so many disciplines that it will probably take some new evidence that turns geology, biology, paleontology, genetics, and perhaps even cosmology on its head to put evolution to rest. Shoot even Behe and Dembski concede common descent.
I have discovered that it has more basis in philosphy than in empiracle evidence, so I question why naturalistic philosphy can have such a heavy influence on science whereas religion cannot.
Because a hypothesis about natural things (empirical things) can be tested. Hypothesis about supernatural things (religion) cannot. You can call that a bias toward naturalistic philosophy if you like. Really it is simply a matter of practicality. If any supernatural untestable claim were given the same weight as natural testable claims, then every scientist would become nothing more then a myth spinner, and science would be nothing but a collection of millions of unsupported untestable stories.