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I disagree and this has all ready taken place to a large extent. Fundamental to this is that it turns out that the repeat elements are such a major component of genomes and this wasn't known until the full genomes were sequenced.

Size isn't everything.

The Science article I linked to article addresses this to some degree in relating how looking only at genes there is very little difference between chimp and human and the reasosn for our differences are in no way apparent. Gene relationships have been extensively examined over decades (hence my comment to you the other day that you have reached the 1980's) and the very high degree of homology doesn't seem to be able to explain the differences in species.

You don't know that. Nobody knows that. Nobody really has a clue if the differences in non-coding regions have much effect at all; and until the relevant knockout experiments have been done, nobody will know. There are literally hundreds of thousands of differences in our coding DNA between humans and chimps.

Breakage and recombination that can be mediated by transposons and repeats elements provide a mechanisms for chromosomal rearrangements (as McClintock was the first to discover) which fits well with an mechanisms for mutations over the course of evolution. This is combined with the epigentic understanding of gene regulation and eu/heterochromatin strucure/function associated with high repeat regions provides a basis for not only the structural chromosomal changes which define species and reflect evolution but a genetic regulatory mechanisms whereby regulation of genes which are essentially interchangable between species can provide for the vast differences in phenotype not reflected in the genotypes (ie the genes are pretty much the same so how do they specify human vs chimp).

Whether transposition is an important source of genome variability is an entirely different issue from whether transposon analysis predominates in current comparative genomics. As I've said a hundred times, the source of genome variability is unimportant to the possibility of evolution; what matters is that variability exist and be heritable. However, Darwin knew no more about point mutations than he did about transposons. What he appreciated was that heritable variability was important.

the very high degree of homology doesn't seem to be able to explain the differences in species.

You don't know that. Nobody knows that.

I agree, which is why I wrote "doesn't seem".

Nobody really has a clue if the differences in non-coding regions have much effect at all;

No, people have clues. I linked to the Science comment article that talked about this.