Hello, I'd like to make some suggestions that would save alot of time (and occasionally frustration) for your users. Keep in mind that all of my suggestions are OPTIONAL and it's up to the user whether they want to use these features or not.

1: When card effects are listed in the box before being put onto the stack, there should be a button or hotkey that makes it put the rest of the effects on the stack in a random order. F7 is nice, but it doesn't work when you have a bunch of different effects going off at once. It's very tedious to repeatedly click cards like that before they're put onto the stack; especially when you don't even care what order they go in.
A good example of what I'm getting at is when you're playing a white weenie lifegain deck and you have Soul Warden , Soul's Attendant , Ajani's Pridemate , & Suture Priest s' abilities popping off every time a creature hits the battlefield.

2: Effects that make you put a number of cards on the top/bottom of your library should also have a button/hotkey that places them randomly, so that if I don't care about the order, I don't have to repeatedly click each card.
Some good examples of this would be Cream of the Crop whenever you cast a powerful creature. Teferi's Puzzle Box , & Abundance

3: Effect's like Cabal Therapy that make you choose one card out of all the cards in MTG should have a search bar that pops up in the same window. As you type in the search bar, it selects the card that is most relevant to what you typed. For example: typing "Par" should remove every other card from the list except for cards that begin with the letters you typed; like "Pariah".
Preferably the search would update itself in real time as you typed each letter, kind of like the Gatherer's search function, although I wouldn't mind if I had to type out what I wanted before manually hitting the "search" button, as the time saved would still be mind blowing.

4. Add an "Attack with all creatures" command. The easiest way I can see this being done is to have a right click menu on each target that is attackable (planeswalker/players) and have one of the options be to send all of your creatures to that one target.

5. Add a command which automatically selects all legal targets for you whenever you use a spell/ability that can select multiple targets.
Genesis Wave is a good example.

6. When paying for X cost spells or abilities, there should be a right click menu on the mana symbols that lets you select different increments depending on how much mana you want to put into the X spell, such as 5, 10, 15, 25, and "all mana".

So far I have played 1 commander game. In that game, several effects changed a cards' controller ( Acquire , Gather Specimens , Corrupted Conscience , Roil Elemental ). Functionally, there was no problem but visually the cards remained on the battlefield on the owner's side instead of on the (new) controller's side.

Also, it was very confusing to me that Commanders in the Command Zone are in the middle of the battlefield, just like they would be if they were actually on the battlefield. However, this maybe optional - I haven't tried to change it yet. 

A few quick-hits after about 2+ hours of playing:

- Not a fan of the little swirly thing denoting summoning-sickness...I much preferrred the p/t turning yellow...it's much easier to see.

- The highlighting of the board denoting who's turn it is should be a little more obvious. You shouldn't have to focus on the board so hard to see this.

- The horizontal phase bar should also show more clearly what part of the turn you're in. Having the current phase 'go black' does not make it easy to see at a glance.

- The card and window movement is a bit herky-jerky. Would like to see a smoother and more clean movement.

- Having a new game open in a new window is cool idea, but having it start partially minimized is a pain. Also would like to be able to save the board set-up and chat window location, rather than having to move everything around every time.

- The new targeting system is interesting, but still difficult to see upon initial action. The spell or ability targeting a creature/player should be easier to see when the target has been selected.

- The Life, Hand, Deck and Graveyard icons are a bit too small and much harder to see than V3. Adding about 50% to 100% more size would improve this.

- Would also like to see the Graveyard become a detachable window like V3. The resizing of the GY is nice, but sometimes you need the cards to be more 'available' to the eye.

Everything just feels so clunky in this version as opposed to v3. As much as I'd like to love it, its quite disorienting, and actually looks worse then v3. In addition, the summoning sickness animations are disorienting, even when they're not on. It feels like they tried to make it as close to Duels of the Planeswalkers without offering that product.