I agree there might be some missing factors in evolution and a few little details that might need to be fixed or filled up. But overall the theory proves to be consistent with current knowledge.
Unless you are a fanatic believer, (claiming creation must be literally as it is written in Genesis or whatever religious text you beileve in) there's nothing wrong in considering that God might be one of the missing factors and that this was just the mechanism He used to create the modern shape of life.
Up no now I haven't heard of a 3rd theory.
The only alternative theory I've heard from people who deny evolution is creationism or some attempts to make a compromise between evolution and creationism.
Nothing that does not involve some kind of divine intervention.
Let's face it there is no solid argument to suggest it might be wrong, there is no better theory, and no evidence at all to support an alternative theory, so evolution remains the best fitting theory that exists today.
Archeopteryx is an excellent example of a transitional fossil. It resembles both, reptiles and birds.
Some scientists argue it could not have flown, others that it must have been a bad flier, limited to flap from tree to tree.
I don't have time to search now, but there are some examples of non-flying dinosaurs with feathers, that apparently were first developed for heat insulation.
The main answer of the "lack of transitional fossils" argument is here:
http://www.talkorigins.org/faqs/faq-...l#transitional
And the explanation of rarity of these fossils and more details.
http://www.talkorigins.org/faqs/macroevolution.html
http://www.talkorigins.org/faqs/punc-eq.html