How would you feel about breaking the lore? Not for the past, but for the future. I've been toying with the idea of Mindy wishing that Jirachi doesn't need to sleep for 1000 years because she feels sorry for the Pokémon not being able to live most of the time. 
And then Jirachi wouldn't have to hibernate after StarFall ends, but can only grant wishes when the comet passes.
This doesn't have to happen of course, I'm okay with staying true to Jirachi's lore too.