To be honest, I can't quite see how what you are proposing challenges Neo-Darwinistic speciation theory.
1. Different species has different chromosomal karyotypes
-It's called mutation. The Nylong Bug is a good example of a frameshift mutation resulting in a new, surviving species. Neo-Darwinism isn't just allele frequencies, or it couldn't account for the rise of new traits. Also, cross-over in Meiosis can sometimes shift homeotic complexes and other gene groups. Non-disjunction (change in chromosone number) is also a result of cross-over. You seem to be completely ignoring the genetic component of Neo-Darwinism. In fact, you seem to be referring to plain Darwinism.
2. Against all scientific evidences so far available
-Ironically, polyploidy is the usual example for mechanical speciation. Endosymbiosis, however, isn't really driven by evolutionary mechanisms. It was simply the establishment of a symbiotic relationship between two prokaryotes.
Speciation was documented several times in Drosophila simply by putting them in different environments for a number of generations. Eventually, when the two populations were put back together, the groups would not interbreed naturally, thus qualifying for allopatric speciation.
3. Lack of explanatory power
-The chicken-egg paradox is just Creation v. Evolution. No scientist will tell you a chicken popped out of nowhere. I don't understand it, you keep using speciation examples to try and disprove speciation. The bottleneck effect is explained by simply allele frequency because it is just a random event resulting in a dramatic shift of allele frequencies, if we are referring to the same thing. The Cambrian Explosion is also not a satifactory example. For all we know there was great biodiversity before the explosion, but those organisms did not secrete the correct chemicals or have the correct conditions to leave fossils. Also, the Explosion is partly due to the fact that land, previously uninhabited, was suddenly an available ecological niche.
4. Un-falsification
- I can't say I understand this argument either. All you need to prove that allele frequency is not enough to create the current biodiversity is to provide counter-examples, as you have done. Also, with simple organisms with fast breeding rates, you can change environments and try to use RMNS to predict what kind of speciation would occur if only allele frequency change was present.
5. Too complicated
-You are aware that the bottleneck effect is classified as genetic drift, yes? Also, you are using the old Creationist technique. "It's real complicated, so it can't be true."
In short, you seem to be confusing part of Neo-Darwinism with the whole. Even the speciation methods you mentioned include non RMNS examples (such as the polyploidy in plants, mechanical speciation). I'd also like to point out that you are also assuming a major conspiracy. The examples you provided are quite evident to most scientists. Isn't it a tad foolish to assume that no Neo-Darwinist ever heard of Polyploidy or the Bottleneck effect?
™ Version 4.2