Your favorite house rules

That sounds interesting. The game seems to have been tested such that adding army card points does not unbalance the game. The base game uses 500 points while Zendikar uses 600 points.

Base card decks are 200 points for 12 cards. For your variant, I would guess that 6 cards for 100 points would be the place to start. My guess is that you will find the 100 points of additional cards would be plenty for a control deck to destroy everyone else.

You might want to try both players adding cards first to get an idea if the larger decks swing the game to being less of a focus on the army cards. If player A can defeat player B without needing to use many army cards, you may have gone too far.

My opinion would be that 3 cards /50 points to one player and 100 army card points to the other player might be balanced.

I say you can "donate" up to 25 points between spells and army. So if doing 500 point army and 200 point spells, you can do between 475-525 point army and 175-225 point spells, as long as they do not total more than 700, but you still have exactly 12 cards.  You can up this "donate" amount but I would not make it more than 50 points if you stick with 12 cards. I could see if you want to make an epic game you can add spells in multiples of 3 cards/50 points, so maybe like 800 point army and 18 cards @ 300 points, being able to donate 100 points either way but stuck with exactly 18 cards. This especially helps in army building as sometimes it is hard to get exactly on a 100 points, but I think if you do the way you suggested where one person has more cards than another it would be unbalanced.

Of course, I also like to be able to add Heroscape armies to them as well and play on Heroscape terrain. There is a whole forum for that though.

I saw this thread, recently and found it very interesting and wanted to add to it. I enjoy seeing others' house rules, as well as I wanted to share my own. I think it helps work out game details, as well as receive some constructive criticism on my own.

My wife and I play the game pretty regularly, always tweaking and learning things. In addition, I recently got my cousins and siblings into the game also.

Here's some of the house rules that we've all played with and enjoy.
1. An army may have between 600 and 625 (or 650, still tweaking that one) of army points. But, a maximum of 3 army cards. This last part was added cause my wife figured out a way to give Nahiri 4 army cards at 600 points, and was just wrecking shop, through attrition.
2. An army built below 600 points may put the remaining points into their Spell deck, allowing them to exceed 200 points.
3. Spell decks can be any quantity of cards, not exactly 12. But, may only have 1 copy of each. (Still toying with that last part.) Spell decks are still 200 pts, unless added to by Rule 2.
4. Hidden Enchants may be flipped at player's discretion. They declare if they want to flip it, once attacks have been declared, but before dice are rolled. If chosen not to be flipped, it is not discarded.
5. The Blazing Firecats may Haste with all 3. (Seems rough, but we've been playing that way this whole time and only just recently found out it was just 1 Firecat that may Haste.)
6. The Cryptoliths yield a height advantage of only 2, or always 1. Meaning, if A is on a cryptolith and B is on flat surface, A is +2. But, if B is on 2 sandtiles, A is +1. If B is on 3 sandtiles, A is +1. All the way up to 8. So, the Eldrazi Ruiner actually is equal to A. (There may be a ruling on the cryptoliths and would love to hear thoughts on this, cause we've yet to find anything. The way we interpreted the Cryptoliths, initially was a height advantage of 10, due to itself and the sandtile it's on.)
7. We don't use turn trackers, except when running the Ruiner scenario. Though, we are toying with a time limit of 1 hour for 1v1, and 1.5 to 2 hours for 2v2.
8. Engaged is only considered if A and B are adjacent AND one of them has initiated an attack.
9. Flyers may walk. (Got that from a thread on here. They said it was from Heroscape, and we tried the rule and liked it.)
10. Cards/abilities may not target "itself" unless clearly stated, basing intention. (ie. there is a enchant planeswalker that give +1 attack to all figures within 4 clear sight spaces. Well, if a planeswalker is a figure, what other figures might there be, except creatures? None. So to give Chandra the ability to target herself with that enchantment seemed unintentional. A clearer example is Jace's Mind Stealer, which allows him to target a planeswalker within 4 clear sight spaces of Jace, and move, attack and use abilities, barring a d20 roll. Jace is a planeswalker, and is with 4 clear sight spaces of himself. Should he be allowed to mind steal himself? The wording seems that would be unintentional. On a freakish good role, Jace could mind steal himself over and over and just keep attacking, if these types of things were allowed.)

After that long winded Rule 10, my mind went blank of any others. Though, I think that's the bulk of them. Many of these don't seem to be game breaking. Most of them were used to handle when an ability or card wasn't clearly worded, or too ambiguous, or unintentional. We try to keep to the heart of the MtG card game, when it comes to rulings. Utilizing concepts such as the "stack" and "priority".

I'm interested at what you all might think of these. Or even if there is a rule that is already stated, that we might have missed.

Let's hope they keep coming out with more sets, cards, figures, and rules!

nerddad is correct that for purposes of attacking or defending, you are either at the same height or you are not. If you are not at the same height, the figure that has the higher elevation gets +1 die. Same Height means that the bases of the figures are on the same level of hexes. If the base of the Eldrazi Ruiner is on the same hex level as the base of a Path Warden, they are the same height. If the Path Warden is on any hex higher than the Ruiner, the Path Warden gets +1 (even though it looks like the Ruiner still would have height advantage).

The height of the Cryptolyths is listed as 4 for the purpose of climbing top the top of the cryptolyth. A figure standing on the double sand tile base of a Cryptolyth needs to have a move of 5 to reach the top of the cryptolyth, 4 to climb it and one to step on the top.

In Heroscape there is something called extreme height that gives a +2, but that is something like 10 hex levels higher than the opposing figure base.

For #8, Engagement should also be considered when a figure attempts to walk away from a figure it has been adjacent to. The figure that is "running away" may be attacked by any figure that it is moving away from. The leaving engagement attack is the roll of a single die with no defense allowed. A leaving engagement attack is optional, the figure being left behind can choose not to attack. This is important in 2v2 games.
This can be important when your opponent controls one of your figures. Your opponent can not move your figure and then 'force' your other figures to make a leaving engagement attack. As a house rule, you can do as you choose, but leaving engagement attacks can be a very strategic element of the game. Move next to a figure knowing that you can't simply walk away with no consequence is an important aspect of movement.

Jass I think if I used your firecat rule variant I'd be unstoppable, I already use Chandra and the prophet to great effect. Stack a spell in there like the one that lets a squad creature act and you have four attacks. I usually buff Chandra before using the prophet so it's four strong attacks. I feel like all three firecats hasting is o. p., but if it hasn't tilted your games to heavily in 's favor then cool. Of course stacking Chandra, the prophet, and the firecats is a pretty good way to take out an opposing planeswalker or pesky hero too.

You may certainly house rule and play as you wish. However, does that mean the Ruiner can 'hide' behind Scion?

Generally protection IS SUPPOSED to be (almost) impossible against a ranged attack. A Ruiner should not be able to hide behind a Scion. On the other hand, a Scion may hide behind a Ruiner. I can understand that is seems a bit off if dealing with two figures that are roughly the same size. There it seems like the front one would block the back one.

The Line of Sight rule as written is important as it helps to determine just what it is to actually be 'in front' of another figure. I'm guessing that you have had some discussion about what makes one figure be behind another. The game deals with Hexes; which means that there are many different angles. Just being 'behind' another figure leaves some interpretation as well.

Now for me, if it were Real Life, I would aim at the one in front and miss, accidentally striking instead the one in back.