1.
Alphabetic "search library effect" I sometimes create large singleton styled decks that are over 1,000 cards. When I tutor for a card it can be tedious to find the card that I am looking for. I know if I hit the first letter of the card I will find it faster than scrolling down.
This method would be even better if when searching your library it displayed your deck in alphabetical order.
2.
Legendary Rule Option- Just like you can select to play with mana burn it would be nice to change the legendary rule mode. I wanted to try the new legendary rule for permanents and at the same time use the old one for planeswalkers. Just to add a bit of customization to it. So perhaps two selectors one for Planeswalker type and the other for permanents with a Legendary type on them.
For example. Your Jitte won't destroy force you and your opponents into the graveyard. But if you play a Jace both you and your opponents Jaces will be put into the graveyard.
3.
Casual Wish Option- Wish cards and "Research"/Development can get cards from the entire card pool of Magic instead of just your sideboard. So far the only way I can do this is play Dev Mode and cancel my actual wish search then just add a card from the Dev mode which isn't too bad but I would like for it to happen automatically.
4.
Wacky formats- Commander/Archenemy/Planechase hybrid modes. A mode where you can have multiple commanders and/or Vanguards. Perhaps a quest mode that allows you to have a commander this will even go beyond the coolness of having quest pets.
I was also considering an idea of creating a new command zone that you can put permanents in. For example the challenge mode opponent starts with a
Torpor Orb and
Eon Hub in the command zone (I realize in quest mode there is a challenge like this that starts with
Eon Hub). In this command zone the permanents effects will act as though they are on the battlefield. But since they are in the other zone you will not be able to get rid of them and you will have to simply deal with the deck. So in a way this would be an extended Vangaurd type of game play.
I know it is a long wish list but I think having these options turned on (not default) would be cool.