I thought about an epic way to implent Semi Legis
After completing the Pokedex you can get special eggs that take very long time to hatch - maybe one year or so - and need to be cared by you.
You can choose which legi egg you want by completing different tasks in endgame.
If you got an egg you can raise it`s IVs and choose the nature, ability, and special attacks by farming materials and beat hard NPCs and stuff.
After long time of caring you get your own epic OT legi that is grown up by your effort and can be used in ubers and normal mode.
you can choose Articuno Zapdos Moltres Mew Raikou Entei Suicune Celeby
Regirock Registeel Regice Jirachi maybe Lugia and Ho-Oh too
only 1 egg at time :)
what do you think ?