Abiogenesis is probably the main point of argument from a scientific perspective (i.e. we reckon that it might have been possible with some lightning and luck to get amino acids, but that's still a very long way from a viable replicator, let alone a complex cell). The shared ancestry is probably the second "somewhat speculative" one (i.e. we don't have a direct line established - there are quite a few holes in the fossil record), but I would agree that it's probably the one where there is more contention (because of its implications).
As for abiogenesis, depending on who you talk to, the probabilities range from "well, if we be optimisitic enough with the numbers, it's pretty good", to "it's so far into the impossible that it could never, ever happen [by being pessimistic with the numbers]." The annoying thing I find is that there are two groups trying to run said numbers (which are kind of guesswork anyway, as we don't have any processes established that we could measure) are those who need to prove it (because otherwise the whole idea of a naturalistic worldview collapses) and those who need to disprove it (out of a need to prove that God's input is required). I think if you take the balance, abiogenesis is actually a fairly good case for a possible place where "God did it" (started life) because it is very unlikely (from our current understanding at least). Of course, this runs afoul of Occam's Razor, as you then have to presuppose God's existence, but most of those of faith that I've met have a good lot of personal experience to back up their belief in God (also, Occam's Razor doesn't actually prove anything, it's just a helpful filtering tool).
So, as for an alternative theory, one (the naturalist) says "this is very unlikely, but it had to happen somehow", i.e. faith in the natural processes, even when there is no evidence for one, nor any known process; the other (the creationist) says "this is very unlikely, therefore God must have done it", i.e. faith in a Creator. When you're dealing with total unknowns (the origin of the Universe itself is probably an even better example, as that's by definition meta-physical (for a strict, not a colloquial, meaing of "meta-physical")), then positing God's existence isn't really any less sensible than positing any other cause, as we simply don't know (and might not ever be able to know).
As for belief, having had discussions with a lot of people on this, I find most self-described atheists actually do have a "faith" in "science" (i.e. what other scientists have said, not in things they've tested themselves) not unlike a Christian's faith in God. Yes, there is a trust of the scientific method, which is different, and while it may (and often does) appear similar, I do understand that it's a reliance on evidence. However, if and when you start to find a point that genuinely challenges an atheist's non-belief in god, they can get very defensive, and unsurprisingly so, because if an atheist was presented with rock-solid proof of God, they have a very big problem with very big consequences for them personally. I have found that most atheists I've met have personal, non-rationally-derived reasons why they don't want to believe in God. (I'm certainly not saying that is the case for all atheists, but it has been the case for most that I have had decent conversations with, and I think is a reasonable question to ask oneself - what are the implications if I'm wrong?)
So, I think that you'll find that a person (anyone) likes to hold a belief system that supports their way of life, and will get quite upset at anyone trying to challenge it, because they don't want to be wrong and don't want to have to change. I think if more of us approached these debates with an understanding that we are treading on potentially upsetting territory, there'd perhaps be a little less angst... (Just winning the argument, even convincingly, is only the start as there will be a lot of re-structuring of thinking required).
Apologies for the long post. :-)