I think the endosymbiotic theory is quite speculative and not based on solid evidence. For instance, mitochondria do not look like bacteria at all and the false representation of mitochondria as bacteria is misleading. There are many examples where mitochondria have very little in common with bacteria except for maybe size and that they contain DNA. Their DNA is in many cases linear and contains telomeric ends, their division is mechanistically quite different. Mitochondria form in reality a complex and dynamic reticulum, nothing like any bacterial cell we have ever seen. Still, evolutionists picture mitochondria as bacteria-like organelles. Also, it is not true that molecular evidence has showed unequivocally that they are derived from bacteria. Phylogenetic studies only show that some mitochondrial genes have a homology with bacterial genes and only show common descent. If we look at the data for Rickettsia, the apparent closest bacterial relative to mitochondria, we see that the data indicate a potpourri of genes from all early branches of Life.
There are also many problems with a mechanistic view on the endosymbiotic hypothesis and in fact there are really no mechanistic explanations. Many questions remain. How to change a bacterium into a reticulum? How can genes be transferred to the nucleus when its function depends on its active import through two membranes and how did the process of lateral gene transfer actually happen. An enormous number of lateral gene transfers has to take place before bacterium is transformed into a mitochondrion (or ‘enslaved’ as the proper anthropocentric current term seems to be), and needs a complete reshuffling of nuclear and mitochondrial proteins. We all know that the eukaryotic genome is complex consisting of many exons and are tightly regulated by up- and downstream DNA sequences. The many lucky accidents include a) an entire mitochondrial gene needed to be b) transferred to the nucleus, c) inserted itself, d) in an unused portion of the genome where it did no harm, e) yet was properly expressed, while f) using a different genetic code and g) still remained functional, h) its product was imported back into the mitochondria, by an i) existing membrane transport protein.
Read here my general critique on the endosymbiotic theory
I address some claims that proponents of the endosymbiotic theory make here.