The academy wouldn't be in Episode 2. JO is set after ROTJ, so how can it have a link to Ep 2? Unless the Yavin system is close to Coruscant, would have to check my SW galaxy map for that, why would they take training off there?
If Palpatine is half the Sith he is meant to be, then he would know the temple used on Yavin 4 for the rebel attack, and the basis of the jedi academy in JO, is according to EU sources, a Sith Temple. That's using the Behind the Magic CD on Ep 4-6, so it seems ironic that post ROTJ that they use it.
Perhaps it is something else that is the small link between JO and AOTC.