I'm not sure "improve the old roll system" is the right way to phrase it, at least in the context that you have any expectation that the bonus roll should be much more likely to give you what you want, if not at least know not to give you what you already have.
Using a bonus roll is effectively no different than if you were to be able to loot that boss twice in one week. Each bonus roll provides the same chances of getting gear from the exact same loot tables as a normal loot roll -- nothing more, nothing less.
So it's an improvement in that you can earn an extra shot at a boss's loot table in one week. But it's not intended to be a system that ensures you never get what you don't need. The random loot system can only be so convenient before it becomes too efficient. We believe chance should dictate whether or not you get something at all and, if you do, whether or not you need still need that item. That philosophy -- specific to boss drops -- hasn't changed much over the years, so it stands to reason that even a bonus roll would follow the same structure.
But with that said, we're exploring ways to make the bonus roll feel like more of a random bonus, without just making it extremely efficient for gaining character power. We understand how it feels to spend the charms and rarely see anything other than gold or items you don't need. So, for example, we could maybe add pets and mounts that would have a low chance of dropping exclusively on a bonus roll.
First of all, I'd like to say that I like the concept of individualized loot system for LFR / World Bosses and the bonus loot system. I like to help people, but the "old system" promoted dropping the undergeared or underskilled, in favor of higher loot roll chances. Individualized looting allows people to take players that would've been left out, but doesn't hurt the person's looting chances. The bonus roll gives a player an extra shot at loot, which is normally not a bad thing ...
Unfortunately, for players that use to play multiple specs (especially now that Bear and Cat are separated into 2 differing specs), it eliminates the ability to perform the role we originally geared for and still pick up off-spec items (in the event we're asked to swap). It hasn't been uncommon in the past for a tank to be asked to go DPS since not all bosses required the same amount of tanks ... and more recently, Healers to go DPS since newer 25m bosses made it possible to drop to 3-4 healers from the traditional 5-6. Previously, I would be able to tank a boss because the group needed a tank (or DPS because they needed a DPS), but still pick up the gear I needed. Now, I have reservations about swapping specs because pulling in one spec means the other spec's gear is no longer an option. This is one of the downfalls of the new looting system: The inability to acquire off-spec items while performing a person's primary role. My suggestion: Allow a person to set what spec they are rolling for (ie. a simple Primary / Secondary option that looks at the person's current primary or secondary specs and rolls based on that spec).
Also, the old loot system allowed items to be disenchanted in case something dropped that no one wanted or everyone already had. Now, there is no option to have it disenchanted since it directly loots into the individual's bag. I have rarely gone to a 25m or 40m where there weren't any Enchanters, so we were always able to use the loot (or resulting crystals from the loot). I would like to see the option given back to the player to either "Keep" or "Disenchant" the item. If this option is too bland for your tastes, I would suggest the options of "Keep", "Sell", or "Disenchant", where the "Sell" option would turn the loot in for an Elder Charm of Good Fortune or (a set amount or random number of) Lesser Charm of Good Fortune.