IMO, it is Alertness and Observation that are your logic problem, not the specific skills. They are Category level abilities classed as skills, if you take them as general skills. I think Alertness does fit that description, but I actually see Observation as a miscellaneous Awareness, not a general one. It covers taking in all the details of a scene *not* covered by the other Awareness*Searching skills. It gives you the sort of information a Holmes-style detective needs for his deductions, but does not impart the special skills of a tracker or a thief or the body language reading required for Detect Lie.
Using Awareness*Senses rolls in place of Alertness will be a little more complex, but you can drop the Awareness*Perceptions category. Another effect is that it will generally replace Alertness skill with something with a higher bonus, but whether that is a pro or con is subjective and campaign dependent.