As the program's creator I see many, many things that could be improved, which includes the whole program. Most of the cards are hardcoded in Java. While I love Java, it makes it very difficult for the average player to create new cards.
Currently all of the decks are stored in one central file and although individual decks can be imported or exported, it is hard to download multiple decks. (In the future each deck will be stored separately.)
Static effects like Glorious Anthem could be handled better. Activated abilities that tap have to be hacked in order to work correctly, the same goes for planeswalkers. Abilities like Hypnotic Specter have to be hardcoded and it would be nice if those types of abilities were handled by the combat code.
And I would really like to improve the AI and truthfully I'm just going to have to experiment to see what works. In order to use algorithms like alpha-beta you have copy the whole "game state" of Magic which includes all of the end of turn effects and everything else which is very complicated and error prone.
While MTG Forge's user interface isn't perfect, I don't really consider it as a negative. Yes, I wish it looked more like a videogame but truthfully I would prefer working on more cards than improving the user interface. In the code that I have written for MTG Forge 2.0 I have abstracted the user interface so it would be easier for me or some else to update the user interface in the future.
I almost forgot that MTG Forge doesn't support the new combat rules. Maybe I could update MTG Forge to support the new rules but it would be a very big job that doesn't look interesting. The hardest part is updating the AI because everything has to work together perfectly.