Mostly I wish they would get their Web API support up to the level of Firefox (ideally even Chrome). It's especially irritating if they start adopting an API, but then only partially implement it (e.g. storage manager API). It might not be noticable in everyday use with standard web sites, but as soon as you have more complicated applications, stuff just breaks.
Also, the update cycle is really a problem - new Chrome versions go out every couple of weeks, while Safari gets updates only with the OS.
This is the kind of comment that they can try to accommodate !