I am among those who think it would be reasonable for the Queen to step down following the precedent recently set by some of her Continental cousins. Having said that, I don't see though how her long reign may have hurt prince William. On the contrary, it seems to me that calls for the sucession to skip one generation will only get stronger the longer it takes for Charles to ascend the throne. In that sense, William is indirectly benefiting from his grandmother's longevity.
The Queen herself behaves in a way that, with all due respect to Her Majesty, looks ambiguous to me. On one hand, she acknowledges Charles' constitutional position as heir apparent, e.g. having him sit by her side at the State Opening of Parliament or sending him as her representative to the Commonwealth Heads of Government summit. On the other hand though, she seems to be raising William's official profile, making him take part in investiture ceremonies and sending him e.g. to Belgium for the celebration of the 100th anniversary of the beginning of World War I (a "Heads-of-State" event).
It may be wild and reckless speculation on my part, but I can't help having this personal feeling that the Queen would prefer William and Kate to Charles and Camilla on the throne and, although she has no control over that matter (which is regulated by law and, hence, by Parliament), she is preparing for an eventual "Plan B" nonetheless.