Berserker turning out to be who he is revealed to be (naw, no spoilers here) actually makes so much sense in hindsight that I'm almost irritated I didn't think of it earlier. The problem is, I thought they already told us who he was back in the first episode, but I'll go back and watch it to find out. Knowing who he is, it now makes sense that he stood on an "annoyingly" level ground with Archer. Considering Gilgamesh's legend, and he hinted to the only person he ever called friend in episode 23 (Enkidu, if you know the legend), the warrior in question would have to be one of those other legendary badasses; the kind of warrior that is always undefeated no matter what trials are thrown his way. Kind of interesting, then, that in the Fate Nasuverse, these badass legendary heroes are BERSERKER classes (Heracles for Stay / Night, et al; our hero here). It also explains why Saber was able to best him...
As for the rest, I adored the Grail ending up being the "careful what you wish for" type of item. It is always so much more delicious when you realize that your miracle turns out to be a cursed gift no matter what you do. In this case, Kiritsugu would have to bear the burden of slaughtering millions, if not billions, of people in order to save the other billions. Not to mention his own beloved family, who are part of the "problem" that needed to be solved (Ilya demonstrates this quite well in Stay Night, etc). In the end, it was too much for even a black and white personality to justify, and the only answer was to make sure that nobody would ever go after this damned thing ever again.
Much to Saber's chagrin... this, of course, is the set up for Stay Night, etc's Saber being a little more cynical about things, and she would only finally understand Kiritsugu's decision only when Denser Than Lead Shirou convinces her of what is right.