Putting Magical Footwear and Stopwatch runes in the same row is a step in the right direction but...
There needs to be more changes DIRECTLY to Stopwatch the rune. (Note: I'm not saying the item. The item, despite popular belief on the circlejerk center that is the Boards, I find fine.)
Don't get me wrong, Footwear and Stopwatch is disgusting together. Getting 1000+ gold's worth out of the combo of these two is ridiculous and I think, despite all the support mains crying about Biscuit and Future's Market now being on the same row, that Riot made a good move making people choose one or the other.
However, Stopwatch is likely to still be a go to rune. People can still get a nice bang for back rune combo with Stopwatch + Biscuits, or still be able to rush early items with Stopwatch + Market. This will probably remain a problem even if my suggestion is considered, but it doesn't hurt to try, right?
Now getting to my idea, it's quite simple really: Make Broken Stopwatch sell for 0 gold.
My reasoning for this is that a lot of champions, or to be more specific, players, are taking Stopwatch without building into 
(
is core on mages and some supports, so this is less of an issue as it's pretty much a guaranteed buy is most cases). What they are doing instead is taking Watch for that one time "SAVE ME" button and then selling it for the amount of gold it gives. While I'm currently too lazy to check for the actual price, 200+ gold makes all the difference for that early 
, that early 
or 
, Hell, 200+ gold can make the difference for the slightly faster 
and such.
Making it so that people can't sell Watch for gold after using it would discourage those that don't plan on upgrading it from taking it, as they sacrifice stats or survive-ability (HexFlash and Dematerializer don't exist) if they still want to go through the Inspiration path, never mind them not going into any of the other four trees. Yes, they are forgoing stats currently by taking Commencing Stopwatch only to sell it after use, but making it so that it sells for nothing should do so even more, no? Would the Save-me-once button really be worth it if they're not upgrading to GA or Stoneplate? Especially considering the constant stats from Magical Footwear? Or, you know, the stats available on every other tree?