How has the theory of evolution changed over time?
It improved quite a bit. To put things in perspective; today most of evolutionary biology is about evolutionary genetics while at Darwin time (On the Origin Of Species was published in 1859), we really had no idea about DNA (the basic structure of DNA was only discovered in the 1950s).
A number of the original claims were found to be wrong though (or off-topic). We've added much more than we've removed though!
I learned at school and in the documentaries like everybody that (to summarize) molluscs evolved into fishes then reptiles then mammals then humans.
Does the theory still make the same claim ?
This claim is not correct (and has never been) or at least is very misleading. I hope your teacher did not really tell you that!
or does neo darwinism only defends speciation where for example all camelidae are related and all felidae are related, but both aren't related
Nope, this would be even more wrong!
Among all extant species today, none are ancestors of others. They all share a common ancestor though. The common ancestor between a lynx and cat lived more recently than the common ancestor between a lynx and an oak tree.
Also, the claim put an emphasis on humans, which sounds like you viewing some kind of goal to evolution or eventually some kind of 'improvement' where humans would be the best or something like that. That notion of good or better is not just wrong, it is off-topic in any scientific discussion.
Some of the clades you mention contain other mentioned clade (for example, humans are mammals), however 1) fish is not a clade (not monophyletic, see this post for an intro to phylogeny) 2) ancestors of mammals have never been mollusc 3) note that the term reptile you use can take two different definitions; a popular meaning and a rigorous scientific meaning (which we use called Reptilia) (have a look at the post If dinosaurs could have feathers, would they still be reptiles?). In any case, no ancestors of mammals were reptiles (although mammals are Reptiliomorphia).
If not, why the famous evolution trees never identify any of the supposed common ancestors ?
I don't really understand this question.
We are able to date pretty well the common ancestors of most lineage of interest through molecular tools. We have a lot of fossil records which, when dated, match our finding with molecular tools. Note that the one most recent common ancestor between two lineages is a single individual (although recombination makes this point more complicated but I won't talk about that here). Of course, we probably never have a fossil of this single individual, but we often have fossils of individuals that are quite closely related to this individual.
You seem to have an extremely biased view of the theory of evolution. I am sorry if your teacher taught you so wrong. The best for you is to simply start with an intro course such as Evo101 for example. Evo101 is short, very introductory and easy to read.