For the bugs and oversights:
When I double click on a trainer or energy in the deck builder, there is no information window that appears like when I double click on a pokemon card.
The card data on almost all of the older pokemon are incorrect.
There are no poke-powers on any of the Base Set pokemon or on a lot of other pokemon from the early sets.
There are no info/explanations on any special energy cards such as Scramble Energy or Warp Energy.
For some improvements:
I think there should be more filters for the deck builder.
Such as: Search by the pokemon's type (Fighting, Water), search by the attacks of the pokemon, how much damage an attack can do, the energy requirements of an attack, and card rarity.
I would like to see an Undo button for when I accidently discard something.
I would also like to be able to use the scroll wheel on my mouse to scroll through the deck builder's card lists.
Over all, the program is great and (with some improvements) it will be better than Apprentice.