Creationism/Intelligent Design is bullshit. God doesn't interfere, he watches all, knows all and sees all. Evolution is easily demonstrated and long proven true. There are no "flaws" in evolution just lack of education.
To answer your first question (I only read the first page) - a quick google search is all you needed to make.
http://www.washingtonpost.com/wp-dyn/content/article/2006/01/18/AR2006011802159.html
"Question: What do you do with half an ear?
Answer: You breathe through it.
That's the conclusion reached by a pair of researchers who say they have found a fossil "snapshot" of the ear partway through its evolution to its current form.
The structure that became the sound-conducting middle ear of land animals began as a tube that permitted ancient shallow-water fish to take an occasional breath of air out of the top of their heads -- at least according to Martin D. Brazeau and Per E. Ahlberg of Uppsala University, in Sweden.
Their conclusion is controversial, as it amounts to a radical reinterpretation of how the ear developed in land-based animals. If it withstands scientific scrutiny, the fossil will be a rare example of an organ glimpsed partway along its evolutionary path, at a point when its function was very different from that of its final form.
Opponents of evolution say such "intermediate forms" should rarely, if ever, exist. They contend that many anatomical structures are too complicated to have evolved step by step. Instead, they had to have been created in their final form.
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"This is another nail in the coffin of the creationist view, in my opinion," said Mark W. Westneat, an associate curator of zoology at the Field Museum of natural history in Chicago. "It is a great fill-in-the-gap story that shows a nice transition stage at an important point in evolution." "