|MadSci Network: Evolution|
You have asked a great question and also given yourself a very good answer. The question you're asking is indeed highly complex and is based in ecology and evolution and as such is our way of summarising a highly complex system so we can comprehend it.
As you said asexual reproduction is highly advantageous over sexual reproduction under certain circumstances and likewise the reverse is true. Many creatures practice both to get both sets of advantages a good example of this is the aspen. When you see an aspen grove you perceive many individual trees, but those trees are genetically identical: they were produced asexually. What is the advantage to the aspen in this situation? Well if you land in a great spot where food is plentiful and you prosper, you "fit" your habitat perfectly. You have Darwinian fitness, you will proper and survive. In this situation the limiting factor to your species' expansion is reproduction. As an individual aspen on this say "new island" you can not reproduce sexually, but you can reproduce asexually. Your offspring equally "fit" their habitat and you are a very successful organism avoiding the downfalls of sexual reproduction (as you mentioned in your question). But as this aspen community you're are now 100 individuals who are identical.
This is a major evolutionary ticking bomb. Diversity is achieved through sexual reproduction, the mixing of genes. In the winter of 1918 a pandemic flu killed 20 million people world-wide. If all humans were the same we would all potentially get the disease and die. But because we reproduce sexually, we are highly varied and some people have genes that protect them. This is true of any evolutionary pressure such as disease, predation and habitat change. So all our aspens could die from one disease. To conclude, asexually reproduction is the best in the short term allowing organisms to rapidly reproduce and colonise new places but sexually reproduction ensures long term survival. If you would like to read further on this note try to find a copy of Slanted Truths, Margulis and Sagan in which there is a Chapter "The Riddle of Sex".
Try the links in the MadSci Library for more information on Evolution.