Tyson pretty much covered it but I'll throw my own 2 cents in...
Whether you strike with the shin or the instep (top of foot) depends on what you are trying to do.
The shin kick is great for slamming home a powerful body shot. You hit with one of the hardest parts of the surface anatomy and, with proper form, you can deal out serious power.
The instep kick is a better option for two specific areas. 1. Head kicks and 2. Stick-and-move. When striking at the head, the aim is to strike as fast a possible because its imparitive to strike before your opponent can properly defend himself. When using a stick-and-move strategy its useful because, even though you cannot deal out the same level of damage with the instep kick as with the shin kick, you are able to strike faster and in a case where your opponent has significally longer arm reach, it helps keep you out of his range.
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I went out the way that I fight. I went out on my shield. That’s it. Done. --Chuck Liddell
My goal is to end my opponent --Carlos Condit