I'm a play tester for another popular tabletop game. One of the things we're aware of when designing/testing/revising new game effects is whether or not that effect, on its own or in combination with other effects, might be "unfun" for one player and lead to NPE.
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Note to Arcane Wonders design team: If you want people to like Academy enough to play it again, don't include resource denial as a primary strategy of one of the only two mages available upon release - especially not in the recommended starter spell book - and don't include a condition (let alone invent a new condition specifically for this set) that prevents creatures from functioning when one of the two mages is supposed to be all about summoning creatures. Hopefully this isn't "too little too late."
I like that you took the time to write out a detailed and thought out topic, but I disagree with a lot of your assessments. "Fun" factor is a very tricky thing to tie down, because it varies massively from person to person. It's easy to label something as a NPE, but there are successful games built entirely around systems many people consider incredibly unfun. Some games are heavily luck-based, some encourage players to team up or betray each other, and some are just outright sadistic. As such, negative player experiences aren't so much a problem as they are an audience limiter. People are either capable of enjoying (or even embracing) such a set-up, or they aren't. I've played games in which I've known without a shadow of a doubt, from very early on, that I had no chance of winning. A lot of people would have been very frustrated by this revelation, but I decided that I would just have fun anyway by doing ridiculous things in-game.
Additionally, you'd have to rip the heart out of Mage Wars to get rid of NPEs. The more complex a game is, the more potential for "unfun" strategies and combinations exist. Mage Wars has a massive amount of potential interactions, and therefore a lot of opportunities for NPEs. But again, that's not necessarily a problem, because the depth of Mage Wars is precisely why a lot of people enjoy playing it. Not to mention that there will always be a chance for NPEs in competitive games. After all, somebody has to end up losing.
I think the most important sentence in your post is that after your wife's disastrous defeat due to your Sleep spell, she was considering rebuilding her deck or changing her strategy to deal with that situation in the future. In my opinion, THAT is the correct way to deal with potential NPEs in Mage Wars. The best part of the game is coming across unexpected obstacles and trying to figure out how to deal with them (either during or after the match). People need to view defeat as a learning experience. Mass Sleep isn't an inherently negative player experience. Your wife just didn't have enough experience to overcome it (a very similar thing happened to me when I first encountered that card).
There always seem to be people who really, really despise control builds/decks in any game that allows them, which I find interesting. However, I disagree that resource denial mechanics shouldn't be included for the Wizard. Mana supremecy and (short-term) creature control are basically WHAT HE DOES. They are the strategies that set him apart from the other mages (as well as all the elemental attacks, obviously). That's kind of like being upset at the Warlock for using de-buffs all the time.
While I understand how it can be frustrating to be blindsided by such a strategy while playing for the first time, new players need to be exposed to it so that they can become better players, and hopefully move on to Arena (and potentially play as the Wizard there). If the Academy mages played nothing like their Arena counterparts, it would probably be even more frustrating for new players, since Academy would be actively teaching them the wrong things. The same is true of Stagger. Players need to be exposed to it so that they know how to deal with Stun and other nasty conditions, both in Academy and Arena.
All of that being said, I have not played Academy yet since I don't own it. If one of the mages, cards, or strategies is noticeably unbalanced, that would be very bad for the game, and Arcane Wonders should take steps to fix that (either by adding new cards to the next releases of Academy, or by changing existing cards if absolutely necessary).
I think that we need to figure out what it is, exactly, about mana denial, and perhaps defensive/controlling strategies in general, that makes it so unfun to play against for so many people. .... Unfortunately a lot of other people seem to get frustrated, feeling like "they can't do anything". If they have less mana, they have fewer options for spells they can cast in a given round.
Perhaps a lot of people don't know how to enjoy that.
.... Maybe if the number or power level of cards which aren't just counters to other cards, and that are physically being put on the table, gets decreased, then it feels like the action is decreasing even if it's actually not. Which might explain why they get bored. Even if the actual amount of action hasn't decreased, there's less going on visually.
This is a great post.