Fare structureI'd prefer a distance based fare system with price bands maybe 2km wide for a first 5-10 bands, widening out to 5km bands. But I doubt that would happen, or be popular until we had a reasonable orbital PT network, so I would support sticking to the current zonal system, with the current discrepancies ironed out (eg: FG train station zone 3, FG bus interchange zone 4, should both be zone 3/4), but maybe do that by adding a little more 'fuzz' to boundaries so that similar to Melbourne there's an overlap area. This does already exist to some extent in some places, eg: with some bus stops in Keperra being zone 3/4 so that passengers on route 367 from Upper Kedron aren't slugged a 2 zone fare to get to the Great Western.
Fare productsI'd scrap the 9 then free, and put in a daily discount. I'm thinking something like 2 paid journeys (peak and/or offpeak) then all journeys for the rest of the day have a 50% discount applied. I'm trying to provide some kind of incentive to use the network more, but avoid the rorting that can/does happen with the 9 then free with people taking deceptive trips early in the week to get discounts on trips to/from work later in the week. Some of these are legitimate, but I know of people who would take a few co-workers go cards with them on the lunch break and use each for a leg of the trip so that each got 1 journey, while only 1 person spent a little time going around on a bus.
Fare levelsI'm not going to specify this, but some of the other fare level's posted look good. Basically dropping the flag fall is the important part. Keep off peak, and make it a 40-50% discount. Not sure if adding in a shoulder-peak fare is worth the complexity, I'd rather just have peak and off peak and maybe make an off-peak fare period before the AM peak.
Fare concessionsI'd keep concessions as they are, but add in Health care cards to make us in line with other states. I'd also aim to make concession go cards 'easier' to get and encourage Translink to work with education institutions to creat a student card+go card (like the seniors card that exists currently). Alternatively, the new smart card drivers licenses I believe have RFID in them. Not 100% sure on that, but I can see civil libertarians not being fans of that.
Ticketing systemScrap paper! It should be go card only, though the network of go card retailers needs to be expanded. If top ups are to be done on buses, then I don't support putting a fee on that, but considering what has been said on this forum about how long a top up on a bus can take, then I support finding a way to make that something not needed, or something that can be sped up.