For example. ToE doesn't explain the diversity of life at all. It simply waves one's hand and states that all are descended from a common ancestor. It in no way explains how or why such diversity exists. Why information exists on DNA? In fact, there's far more that's not explained by ToE than is supposedly explained.
Darwins thoughs where lead by the very question of diversity , the classic evo quote "if god made all creatures he love bettles best "
ToE clearly tries to show mechanisums for one line to diverge leading on to multiple lines ....remember it is a Theory
ToE came before DNA discovery , DNA compliments the ToE by providing a method of inheritence . . . and difference with in a population of traits .
ToE does not try to explain DNA ..that is science call genetics , and genetics is making large steps in explaining the infomation carried by the DNA of a organisum ...
ToE makes use of the knowlegde from genetics to look at the detail evolution .
One of the difficulties of fully understanding ToE is it is a multi disipline theory , it draws on genetics , biochemisty , ecology , geogolgy , nuclear physics , archology , cellular biology , planetolgy , and a host of other , you need to be able to read each of these areas to get the coherent picture .Most people are simple not that widly educated or have time/ interest to look so wide . Personally , with a BSc in biochemistry , i find there are many areas i need to stop and find a few books to understand a asspect of it .
Also the ToE operates over vast distances , of time , who can visualize 1,000 years ... a blink in the ToE , tey 5,000 , 10,000 , 100,000 .
lastly ToE suffers from being popular , i do not mean in the CvE debate i mean in the media , and so we are all given very dumb down versions of it OR equal bad portions of it out of context . e.g.
Dinosaurs are TV stars , yet every prog lump the curent Favs together reguardless of evidence .