When I use Typhlosion's "Flare Destroy" attack, which player chooses the Energy card to discard from the Defending Pokemon?
The player that used the attack gets to choose which Energy cards get discarded from both the Active and Defending Pokemon.
Source: HeartGold & SoulSilver FAQ (2010-02-11), PUI Rules Team (2010-02-11)

Relevant cards

Note: All applicable cards may not be listed below.
HGSS1_110
HSP_HGSS09
HSP_HGSS09