I think a large part of the problem with the conversation between game pacing and Stopwatch, as it has been happening thus far on the Boards, is that some users have been accusing players of hypocrisy for criticizing both early tower dives and the item, even though the latter lets champions survive tower dives better. The main reason this kind of reasoning is wrong, also unhelpful and needlessly divisive, is that Stopwatch is being criticized not for stretching out the pace of early fights, but for being too powerful relative to competitor runes, and overpicked as a result. It is therefore a change that may have partially alleviated one common problem, but that has introduced another in exchange, so it doesn't really resolve things in the end. Moreover, when players criticize early tower dives, they specifically point to the fact that towers, which are designed to act as a deterrent to aggression at least in lane, are often incapable of inflicting meaningful enough damage to champions who dive even very early into the game, meaning that they never truly provide a measure of safety at any point in the game.
As for games ending too quickly, I think Stopwatch actually contributes to the problem, because as many players have already pointed out, Perfect Timing and Magical Footwear combine to reduce the cost of builds by 650 gold. Adding Kleptomancy on top of it all thereby accelerates the pacing of games even more, as it makes champions who spec into Inspiration complete their build at a much faster rate. From what I understand, Riot is planning on putting free Stopwatch and free boots on the same rune tier, so that should help with things somewhat, but beyond that I still think Perfect Timing might need a nerf, whether it be to the delay before obtaining it (so that you'd get it later in a match, thereby offsetting the advantage of receiving an item otherwise valued at 600 gold), to the gold it contributes towards future items, or even just to the stasis duration, so that it doesn't quite provide a free Zhonya's active.