1. We can tell a lot about a creature from its skeleton. Size, approximate weight, how it moved, what it ate (generally speaking), etc. And some fossils include impressions of exterior features, feathers, scales, skin texture, etc. Depends on the type of fossil. Do we know everying about it? No, of course not, nor is anyone saying 100% this is what something looked like - but we can make some very good deductions from skeletal remains.
2. Homology doesn't prove ancestry, but in combination with other evidences can be taken as supporting evidence.
Apes: I'm rolling with scientific consensus on this one. Sorry. And peer reviewed journals are preferred in citations. It may prove to be wrong... I expect someone who can prove it is, will get a nobel. But in the meantime, the vast majority of evidence points clearly to our common ancestry with the other apes. We can argue about which hominid belongs where in that ancestry, and which ones were evolutionary dead ends, but the principle remains unchallenged - only the specific path we took is in question, not that the path exists.
The phylogenetic tree has been supported, and where it did not mesh with the earlier fossil based tree, that one has been re-categorized and reassessed in light of new evidence (who knew that whales were more closely related to cows ... pretty cool). That self correction is what makes science great. New information = re-assessing our understanding. The links you provide do not refute evolution, they refute that there is a simple tree we can follow. There may be complicated networks of interrelated evolutionary chains (per your Biology Direct link), but the principles of evolution itself are not in question. (see page 11, the conclusion)
Looking “beyond the TOL (tree of life)”, we are inclined to believe that the use of the TOL as a heuristic to organize and analyse comparative data and partial trees will be with us for the long haul. Whether there is life remaining in the TOL beyond this usage or whether it has to be replaced by new, probably web-like representations of genome evolution, is a question of major interest for phylogenomic studies and will continue to inspire research far into the future
Again, I'm not basing this simply on how things look. There is more evidence than our physical appearance (and in the case of the apes, our genetic code) that makes use group man as an ape.
As for your last picture - it rather misses the point of population sizes 5-10 million years ago, as well as the rarity of fossilization in general. But the fossil record is more complete that it lets on, and when supported with other data and evidence, becomes very hard to simply dismiss.
We are constantly learning more, and reassessing what we know. When you show me a way to test for creation, and explain how it accounts for the mountains of evidence we have that points towards evolution ... we can do that too.
