Is the object of Elements to design a cleverly strategic deck and outwit and outluck your opponent? Or is the object to log the most hours possible so you have all the options available to you?
I would completely eliminate the deck building/rare card system altogether. Since upgrading and winning cards are simply functions of time spent playing, having 'rare' cards only rewards people who spend the most time playing rather than the people who have the best strategies. The emphasis on deck building causes people to ignore every aspect of the game except how to win the most money the fastest; so they can upgrade the cards they need to compete.
All cards should be available to all players - just like the trainer. If you want to include 'rare' cards that have to be won or bought, then those cards should only be different versions of the common cards - not clearly better than the common ones. For example: a 'Rare' Lobotomizer would maybe cost 3 aether to activate, instead of one, but could lobotomize protected creatures. This would not only make the playing field more level for new players, but would create much greater variety of decks. People would be forced to consider which cards to use, rather than having the obvious choice of a tower over a pillar, for example. Zero-sum games are always more fair than inflating ones.
Eliminating the 'rare' structure would also have the bonus of eliminating farm decks from the T50. No rare cards - nothing to farm.
Deck-building also discourages people from playing different types of decks. Even if you use the trainer to test your deck before spending money on it, it is far too costly to overhaul a deck - to completely change mark/strategy. If you want to actually use the deck you designed, you must have the accumulated money to buy it. This favors players who - in many cases - have done nothing but use someone else's deck design to farm coins. Also, not everyone knows about the trainer, so it strongly advantages players 'in the know'.
The selling price of a card should be equal to the cost of buying/upgrading it. Why should you have to go from a fully-upped deck to a 1/2-upped deck due to the money lost selling towers, then buying pillars and re-upping them to towers? Is this some way of punishing a player for changing their strategy?
"You can go to the trainer and experiment all you want, but in order to actually play the game with your deck design, first go grind AI3 for about a week..."
This is not the viewpoint of an impatient noob.
I've been playing this game since April '09. I've played nearly 5000 games in that time.
EDIT: And don't even get me started on rush decks.
EDIT: Added stuff about T50 farming.