I would have to say that forcing the d/l counter back to 0 is probably not the best idea. Recently I uploaded Translucent with colorisation support and optimised (16bit and 256 color bitmaps). Then when WBXP beta came out a couple of days later it caused massive slowdowns when viewing the skin in the preview window and the colors were not applied.
I was forced to change all those bitmaps back to 32bit and update it to fix that.
Then XP Copper was released with XP stuff. Of course I wanted to add that. (Another update)
Then I notice the pause button functions as a play button in the WBamp section. (another update)
Then Brad tells me how to speed up the skin by 20%. (Another update cos I don't want WB blamed for speed problems caused by my skin)
If people know the d/l counter will go to 0 they will just submit the skin as a seperate download or they will wait for a week.
Consequence of waiting for a week:
Skinner uploads skin Monday (week 1)
Just after uploading the skin they realise they have some things set to stretch instead of tile which hampers performance and update it.
It gets 15,000 downloads in a week
Meanwhile the skinner notices something they need/want to update which is hampering performance or just looks ugly on Wednesday. (D/L) count is 5,000
They think 'oops I can't upload for 2 days'
They wait for Monday of week 2 and upload the skin.
10,000 people download the skin again. (5000 didn't like it after all

)
If they could have updated when they noticed the problem those extra 10,000 downloads would not have existed causing less bandwidth to be used
Maybe after 3 updates in a week the skinner would ned to submit a valid reason to update it again?
Or they could be put into a separate holding area for the admins to check separately knowing they are updated skins.
Just suggestions and probably not very good ones.
Wow that was long. Must go rest!
Oh and paxx's solutions sounds good 'Updated skins'. However there will still be some how will update lots to appear there as it makes their skin more visible.