I voted for these five, though I could have picked 7 or 8 of them:
1 Endgame PvE content
2 More PvP content
3 More Quests, possibly daily
4 More balanced shards
5 More ways to gain rare cards
Honourable mentions (almost voted for these)
6 Improved AI
7 Achievements
8 RPG elements (pets, levelling up mark or skills, perks...)
1) I've been playing this game since March 2011. I've had a lot of fun with it. However, a month or so ago I finally completed my set of cards other than nymphs/marks, and so I have a lot less incentive to play, now, because I have nothing to really work towards. Typically now I will play my 3 oracle pet matches, my false god prediction, look for league games, but usually that's about it, now. Occasionally I'll still play plat arena or FGs using silly decks, since I no longer care if I lose score or electrum, but that's not frequently. If there were, for example, a higher AI level than FG or plat arena, I'd play that, even if it had no rewards. (of course, rewards are good, too, but I'd just be looking for a challenge)
2) PvP right now consists of 3 options, pvp1, pvp2, and duel. PvP1/2 mostly consist of newer players, and I don't find it fun to EM some guy's unupped monolife starter deck in pvp2 who's played maybe a few dozen games total with my fully upped speedbow, for instance. Duel requires that you go to chat and set something up, though that usually means the quality of game improves, either because you can agree beforehand on certain house rules, or because you can pick your opponents, and so on. It also increases the amount of time it takes to set up. Also, while we do have PvP events on the forum, we have no in-game supported events of any kind. Other CCG games, for instance, have in-game supported tournament systems, so that any time you can get the minimum # of players together, you can set up and play a tournament hosted by the system itself.
3) This would be great. Right now, I primarily play two CCGs online (elements being one of them). The other one, which I will not name for competitive reasons, has two daily quests every day. You will notice after awhile that they repeat, with minor variations, once you've been around for a month or so, but there's still something. In that game, they serve primarily as a way to get in-game currency, so the analog to Elements would be an electrum bonus for beating them. Daily quests could even be used as an indirect sort of tutorial. For example, you could customize the AI quite a bit for such things. Maybe you could create an opponent with insane hp, like 300-400, but that has a very very slow deck, and the player would have to try and figure out what deck beats that best. Or maybe there's another deck with something like a 5x mark and triple draw and tons of removal/control but it's only got 50 hp, so a really quick rush or difficult to counter strategies like quints or whatever might work, and so newbies (and veterans) would be required to figure out how to beat them. Of course, there's other ways it could be done (maybe they only get a certain number of attempts at the quest before failing) and the possibilities are nearly endless, but it requires a lot of thought to be put into the quests beforehand.
4) Several of the shards are fairly balanced. Focus and Sacrifice are widely considered to be too strong, however. I'd argue that those two are way beyond overpowered. Some of the others are quite strong, and borderline OP. Others like void, gratitude, divinity, and readiness are fine, although spamming readiness on a time creature shouldn't act like it does. (or else the card text needs to change to match ingame behaviour, but if it behaved as written, it would be better)
5) This kinda goes with other stuff mentioned, but having other quests, etc, to obtain rares or even nymphs would be great. Also, in future, other rare sets could be created that are only quest-winnable. For instance, Zanz could create a rare shield set, which aren't won via oracle or spins, but can be won through quests.
6) A smarter AI would be nice, but it's extremely hard to code a smart AI, even for a simple game like this. I'd rather see easy ways to just make the AI harder, like more hp, draws, pets, etc, and focus on the first five things.
7) Achievements would be fun, but not necessary. We can, after all, set our own unwritten goals and try to achieve those. (beat 20 FGs in a row, gain 10k score in a day, etc)
8) Pets/perks/etc would be great, but unless we have more pve/pvp and other content like that first, all we're doing is making the game easier. If we add more tools to win games, we need more difficult situations in which we find those tools aren't enough to win games. Therefore, other endgame stuff needs to come first, otherwise we'll be running things like Instosis with trial reward: ban black hole/pest to farm :p