I see your point, but I didn't give you the full story....
The Phantom Pokemon are the "elites" (I use that loosely) of their respective types. When a Pokemon get KO-ed, the Phantom Pokemon take the form of the elite Pokemon and ensure the safe "passing" of the Pokemon. They are like guidance to the afterlife.
My fake commercial might make more sense:
There is a lone Togepi crying over a deceased parent Pokemon in a cold graveyard at night. You see the spirit of Togekiss above the tombstone smiling over the Togepi, when an evil spirit attacks the Togekiss spirit. The Phantom Heroes posses a Pokemon, like Arcanine, and assist the Togekiss.
And at the end, the announcer says: New, Pokemon
hantom Heroes, fight from beyond the grave, get revenge for the fallen...in stores now. 
Plus, it would be harder to get out the Phantom Pokemon if you could only play them when a Pokemon of the same name got KO-ed.
P.S. Thank you.
The Phantom Pokemon are the "elites" (I use that loosely) of their respective types. When a Pokemon get KO-ed, the Phantom Pokemon take the form of the elite Pokemon and ensure the safe "passing" of the Pokemon. They are like guidance to the afterlife.
My fake commercial might make more sense:
There is a lone Togepi crying over a deceased parent Pokemon in a cold graveyard at night. You see the spirit of Togekiss above the tombstone smiling over the Togepi, when an evil spirit attacks the Togekiss spirit. The Phantom Heroes posses a Pokemon, like Arcanine, and assist the Togekiss.
And at the end, the announcer says: New, Pokemon
Plus, it would be harder to get out the Phantom Pokemon if you could only play them when a Pokemon of the same name got KO-ed.
P.S. Thank you.