Real reason broken stopwatch is broken.
Broken stopwatch in itself is a VERY strong rune. Don't get me wrong, it still provides massive dive/survive potential for free. Its main downside however, is that its a ONE time use.
The problem is that the game snowballs and ends so fast that it only takes one dive kill + stopwatch to snowball the lanes.
Obviously everyone's going to take runes that have such a massive impact on the early game, when the early game more or less decides the entire game.
The game length/snowball potential is the real problem: all because of the mobility and damage creep. Champions that have essentially no resources and can poke for insane damage and 100-0 you with one combo even if you are ahead are the problem. ADCs that no longer have to kite, but just right click to make up for assassins having so much damage are the problem.
YES, remove stopwatch - its broken. But don't let this distract you from the real reason - the way the game plays right now.