Well, there are a couple of things to look at.
Tactics/<whatever> can help you figure out the best way to attack something, or defend yourself against being attacked. So taking the best 2 out of 3d6 can definitely help you figure out what's going on. However, the big benefit of tactics is that you get to add its rating directly to your initiative (in certain situations). There's no rolling involved in this, its just a straight bonus, so Natural Aptitude won't apply. Its also a complex skill, so your cost for the Natural Aptitude is going to be +5 TP.
Combat Sense lets your roll initiative as if its NA (3d6, take best two), but it also provides additional benefits, such as reducing stun and surprise modifiers, and can help (if your GM allows) in stressful non-combat situations as well. Is also "only" a +4 TP cost.
I would think that unless your character is the guy that's always coming up with the plans, then your better bet is Combat Sense. After all, you get the initiative bonus from Tactics without having to roll anything. If you're the guy that's always going to be coming up with plans, or looking for flaws in your opponent's plans, then Natural Aptitude Tactics might be useful, but its use is going to be pretty limited.
Of course, all this is assuming I'm not missing anything obvious :)