I was giving this a lot of thought last night, and I've come up with some more ideas/suggestions:
The bounties/contracts should be daily, available early on(say level 50 or so) and offer the various random challenges discussed before. Ie, kill x faction(Jedi, Sith, Rebels, etc), defeat a fight with x character on your team/defeat a fight vs x character, etc. They reward you with decent stuff, especially as you go higher and after harder bounties. Even early on though, 1m credits, 5 shards, decent gear, handful of crystals, etc should all be rewarded for completing your bounty.
Part of the bounties will be a time limit, usually 24hrs, but sometimes 12, sometimes 36/48/60/72. Thus, you really gotta hustle to collect them, and you may not be able to do more than a couple per day, depending on how hard they are.
Bounties also earn you reputation points. These can be used one of two ways: Spent in a special black market shop or to open up 'bounty battles'(wip name lol).
The shop is pretty much top of the line stuff, but it needs to offer everything on rotation. Ie, credits(in a massive amount, like 10m), crystals(at least 100), shards(both character and ship, and all characters other than Palpatine, Yoda and K2 and like 10 or so at a time), Zeta materials(5), and high end gear.
Or you could spend them to unlock bounty battles. These are progressively harder fights with really sick rewards, but also a special 'bounty' per fight.
An example: First one you unlock should require level 80, 6*, gear 8 characters. You should have about a 75% chance to win(With minimum pre-reqs, of course). Hard, but not overly so. This is key, we want the first node to not be so difficult it turns away casual players, yet still offers hardcore folks good rewards and a solid challenge.
Rewards for this would be 15-25 shards, crystals(a good amount), training droids(4-5* ones and like 50 of both character and ship), and level 9+ gear.
The second one you would need to be level 85, 7*, gear 9(or even 10), really good mods, and all your abilities should be level 7. Meeting these requisites means you have a 50% chance or so of winning. Rewards would be the same as the first battle(greater amounts and better stuff), but also a few mods of the highest level.
The third one would require you to be fully maxed out on everything(Mods, zeta abilities, gear, etc).
As I said, there would also be a special 'bounty' per fight. These should be pretty challenging, like some of the above examples of win without anybody dying, have x kinda sucky character on your team, win in an allocated time(if you don't, you can still complete the base battle), etc.
These get you badass rewards, but they rotate each day(or even week). Ie, day 1 is shard day, and if you complete a bounty, you win 50+ shards. Day 2 is crystal day, 1000 crystals, etc. You could even unlock a character(3 or 4* ones to make it worth it), but those would require a pretty decent challenge.
Anyways, sorry for the long post, this kept me awake for a good while last night, lol.