I think the draft format was fine back when the game was released. It was just hard enough to put together a deck with a good mix of solid minions and a few combo cards. But with all of the new cards that have been added since then, there is just too much variance in the card choices now, and a lot of those new cards are very situational or are extremely ineffective without the proper set of supporting cards. This has all led to arena deck drafting be very much luck based, there isn't nearly as much skill or strategy involved in it as there used to be.
Something as simple as making each card selection a choice between 4 cards instead of 3 would make a huge difference. I'd also like to see them add the ability to essentially 'mulligan' a set of cards (i.e. you don't like any of the choices, and you can throw that set of cards out and get a new set to choose from). This would have to be limited to something like 5 mulligans per draft obviously.
Suggestions like these have been floating around for a long time, but I really think its time Blizzard gives it some serious consideration. This problem is only going to get worse as more and more cards are added, and I suspect Blizzard has another big expansion (like GvG sized, 100+ new cards) coming within the next 3-6 months.