Dude should have picked Sky Dragon Eyes, even if they had eaten all of the available skill points. It might have led to an exceedingly rough start, but on the other hand, if he had survived the start, they would have probably been astronomically useful. They can't cost full 100 SPs for nothing. Who knows, maybe they would have allowed bending the weak-minded into his service. Furthermore, dragon eyes should bring a degree of dragon lineage with them, free of charge! How else would one possess them? I guess as grafts, but that would be an extremely strange starting condition.
@blamo He knows how to fight. Not only was he attending dojo back in Japan, but he also has fighting related skills/abilities. What use would they be if they didn't exist? In fact we know the abilities do exist in general after this chapter (he has Light Element at lvl 2 and even the shopkeeper noticed he had affinity to the appropriate spell book). So, the combat skills ought to be there as well, injected into his new brain. That being said, I'm not going to call him a coward because of this. He already showed he has some backbone by rejecting the preprogramming and not following the others to the default location. Now, he shouldn't go into the dungeon if he doesn't yet feel like it. There's nothing wrong about getting used to the world first. After all, he's literally born yesterday.