*sound of clapping*
Well said, Volteon. I don't think Bug-Types are weak, they're just used less than other types. Any type of Pokemon can be strong or weak.
We shouldn't judge a book by its cover (i.e. it's type)
Anyways, here's my idea
I would make 2 uber legendaries. A great kung fu master pokemon (with an ability that makes Physical Attacks halved in power) said to be able to kick the Earth to the sun, and a Poison Slime Pokemon (with an ability that makes Special Attacks halved in power) who turns everything around it into complete nothingness (except for, of course, other legendaries).
But, as usual, you can only get one of them per version. But, like all the 3rd gen and 4th gen version, there will be a 3rd uber. Only that it would be way harder to obtain. Like, say, you have to see all the pokemon you could see in the game before getting a "National Dex" (including all previous generation pokemon except the legendary pokemon, which will all be seeable in the game if you look all around carefully enough) and then make the player go through a 100-room dungeon where you lose all your other items and get 10 Full Restores, where you'll have to fight a lv100 EV Trained and Max IVed pokemon every room with only 10 Full Restores (some ubers) before you get to the last Bug-Type Uber.
Rayquaza and Giratina? Bah! Anyone could get them.