It's a tough problem to get your head around. Sure, the premise makes sense- that the Monte Carlo heuristic plus the UCT tree-exploration algorithm balances promising nodes with uncertain ones to intelligently expand the tree. But tweaking that algorithm usually hurt performance more than helped, and the tweaks that did improve gameplay were non-intuitive.
One semester our goal was to improve the random-playout generator to play slightly more human-like games. It turns out that almost any play enhancements made in the Monte Carlo simulator crippled performance (for instance: instead of playing randomly, search the board for an opportunity to capture the opponent). The best result we had was achieved by applying the capture-if-possible heuristic on only two positions per random move (ex: at the beginning of the MC-simulator's move, pick two positions randomly- if moving in either one captures the opponent, do it). Applying that heuristic on any more than 2 positions per move made the random games play out more slowly than it was worth. Needless to say, a lot of time was spent testing our tweaks (which itself was quite time consuming).
It was frustrating to see our initial seemingly sensible tweaks cripple performance, and it definitely took some time to calibrate ourselves to the problem at hand. But I probably learned more about programming while working on Go than in any other 3-semester span.
Peter Drake's Orego player is a great starting point for exploring the UCT algorithm (Peter Drake wrote a popular Java textbook you may have used in undergrad). I highly encourage people interested in AI to check it out: