I disagree with all the people saying that conditions should be (or should have been) simplified to reduce complexity. While some conditions are similar, they aren't exactly the same, and eliminating the differences between them would seriously damage the theme of the game. That strong sense of theme is a really important factor that contributes to my personal enjoyment of the game.
As for what I would change, if given the chance? Hmmm......
1. Replace effect roll die with something more consistent. I'm not a huge fan of the variation in regular attack die either, but at least that doesn't usually lead to all-or-nothing situations that might single-handedly determine the game. I strongly believe that most players avoid using a lot of utility-based attack spells solely because of this inconsistency. People don't want to risk an entire game around whether [mwcard=MWSTX1CKA01]Surging Wave[/mwcard] will actually push a buffed [mwcard=MW1C06]Brogan Bloodstone[/mwcard] away from your mage. So instead a lot of people just spam the highest damage attack cards (force hammer and hurl boulder) and ignore the effects. There are other ways to balance out powerful effects like stun: you can either have extra target restrictions on the card itself or just make it cost more mana.
2. Create a movement stat for creatures. This would have gotten rid of the necessity for a couple of keywords (fast and slow) and also allowed for more creature variety as well as more effective kiting strategies. Imagine a creature which had 4 movement (balanced out by low health, perhaps), allowing it to run around and pick off weakened creatures.
3. A split online / tabletop focus. Bear with me, this one's a bit weird. I love playing Mage Wars in person, but a lot of the people who I would regularly play with either don't live near me all of the time or are too busy to drive to my house (or vice versa) just to play a board game. So I would have added a way to keep track of exactly what cards players possessed, and let them use those cards to play online matches of the game (either with their friends or in ranked tournaments). For example, Arcane Wonders could have included a serial code in each box of the game that would unlock the cards in that set on a player's online account. Then players have the best of both worlds: they can play in person or online, whichever they prefer. Creating such an online/offline system would also have had advantages for the game itself: the devs could set up playtesting events online to help balance cards before they officially come out (and are annoying to errata). Yes, technically players can use the fan-supported OCTGN system, but that shouldn't have been necessary in the first place.
4. Double-sided Domination tiles that come standard with Arena. In hindsight, the variable terrain introduced with Domination makes the game a lot more fun (as a semi-casual player). Packing that into the base game instead of the traditional board could only have helped its initial popularity and portability. What I still don't understand is why the new tiles aren't double-sided. When everything else about the game from a component standpoint feels so polished, the waste inherent in only using 1 sided tiles is really bizarre. Two-sided tiles would also have allowed the devs to make every tile have one unique effect side as well as a regular side. That way players could choose to have an all normal board, complete chaos, or anything in between. Sadly, I don't expect this to get rectified any time soon, since new Battlegrounds releases will probably need to be compatible with Domination tiles.
5. Regular Release Schedule. Yeah, I'm being a bit cheeky, but I also know that the long, LONG wait for Paladin vs Siren has seriously hampered my enjoyment of the game. The smaller releases just haven't been the same, and the lack of new mages makes the game more boring. There are still SOOO many possible mages that the game hasn't covered (*cough* frost mage *cough*), which makes it even more frustrating that we'll have been waiting 3 YEARS for new mages by the time PvS is roughly estimated to finally come out (DvN released Nov. 2013). That should never have been allowed to happen. At some point you just need to lock certain stuff down and move on to only minute balancing instead of constantly redesigning everything because it isn't absolutely perfect (which is what I'm betting has at least contributed to the delays). I can't speak for others, but I'm not willing to wait another 3 years for Barbarian vs Sorcerer (or whatever it will end up being) to roll out. I'm not asking for monthly releases or anything crazy like that, but getting a new set of Arena mages out the door at least once a year (along with 1-2 minor Academy releases and perhaps a Battlegrounds or other expansion) should be considered the bare minimum.