I like this idea! Like others have said, it would be tricky and need some work but no auto-fail games because someone went afk? Awesome!
When reading about the masteries/runes/items issue, a couple of ideas popped into my head. What if the new player spawned as the same champion but they:
a) when accepting to be an afk fill, they are shown the other champions on their and the enemy team so as to choose an appropriate build
b) started the game off with a gold pool as where the original player left off. i.e. Master Yi had accrued 4k gold. AFK fill has 4k gold when they jump in.
c) they would take on the score and experience of the former player. It would kinda suck to jump into a 0/5/0 game though but part of the risk of a shorter queue?
d) could choose from a list of games (with no information about how long the game has gone on and such) and which champions they could play. I may own LeBlanc but if I queued and had to play her, I probably wouldn't help my team any more than the AFKer ;)
Also, I'm not sure if this would give the player jumping in an unfair advantage. Let's take our Yi. AFKer had accrued 4k gold. Say he bought Boots of Mobility (1000g) and a Wriggle's (2000g) and spent the rest in wards and pots. The AFK fill could come in and buy I.E. (3800g) off the hop. That would be a huge damage spike. Iunno. Just some ideas!