1. Obviously chloroplasts and mitochondria don't live idependently. No one suggests they do, and certainly no theory suggests they should, or could.
That's what you have been arguing from the start, that they were parasites and hence were individual organisms which were captured or intruded themselves into eukaryotic organisms and entered into a symbiotic relationship with them. The above is an admission that I am correct and your argument all along has been false. Thanks for being truthful.
6.I don't understand why you think this is so. It seems to me it would be more inexplicable (from an evolutionary perspective) if they were all the same.
Pretty simple really. What the genetic code does is it translates from the DNA to the amino acids used to make proteins. To change the genetic code successfully without killing the organism and totally destroying functioning you have to do two things - change the DNA code in all the proteins and change the way the code is read into amino acids. You thus need two things to happen at once and of course that is impossible to do gradually.
5. Why is this such a problem? Never heard of DNA transformation? There's a little field called "genetic engineering" that's based on it. Bacterial DNA gets worked into eucaryotic nuclear DNA all the time.
Well, that's the problem with your answer "Bacterial DNA". Yes bacteria can grab DNA from other bacteria and it is often done experimentally BUT EUKARYOTES ARE NOT BACTERIA and do not do that and such has never been observed. So you are getting desperate. First you had said they were free-living parasites, now you see such cannot be said so you pull this from bacteria which does not apply. Methinks you have lost the point pretty decisively.
In addition to having refuted your counterarguments decisively three of my arguments which are also pretty decisive you were unable to respond to:
2. the destruction of their ability to exist as self sufficient entities once they were supposedly taken over by eukaryotic organisms.
3. Why the mitochondria of all surviving organisms lack the same abilities of self-sufficient survival in all species.
4. Why there is no stepwise loss of abilities in even the most primitive species.
So, regardless of your rhetoric, I have proven my point quite well that this endosymbiosis of mitochondria and chloroplasts is just more evolutionist nonsense and more fact-free pseudo-science from people who really should know better.
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You are DEAD wrong (again). Any decent molecular biology text book will cover the topic of "transformation" in eucaryotes (including animals). Heck, you can get genetic material (including bacterial genes) into animal nuclear genes simply by microinjecting naked DNA into the nucleus. You don't even need a plasmid or virus.
I'm afraid I don't see the logic behind any of your other points, so I'll let them be.