Disclaimer: My K/D is about 0.97 as of this post. I've never played a competitive FPS before Destiny, and I've only been in Crucible for a little over a week. I am experienced with competitive balance and meta games in general from both play and theory. I'm very serious about improving, but if you want to brush off what I say, feel free.
Having experienced using Fusion rifles in the Thorn bounty, and generally theory crafting on how to improve my skills, I think it would productive to share what I've discovered about them. I find that they're best used as Defensive Weapons and suspect that they're vital to Destiny's metagame, so long as they're limited to that niche and not used as offensive weapons.
Without FRs, I think the metagame would likely evolve into a Shotgun Rushfest; ARs simply don't have enough killing power to stop a player from rushing from Mid to CQC reliably, Scout Rifles would get no play, and Hand Cannons have too steep a learning curve to be a strong counter for all but the best players. A hardcore metagame would evolve, and while that sounds good on paper it's a death sentence to a community's growth. Newbies would get frustrated and quit before they can improve. I think the Devs have figured this out; that's why they haven't been nerfed.
When I score a kill with a Fusion Rifle, it's usually because of one or more of the following:
1) My target wasn't using cover effectively, or there was no cover to be had. Fusion Rifles are meant to punish players who are not conscious of cover in a game with otherwise long TTK.
2) They attempted to rush me with a Shotgun from mid range. Again, this is exactly what they are meant to do for the metagame.
3) I flanked them or they were otherwise distracted. Any gun would do the same.
I've also noticed the weakness of Fusion rifles while using them and fighting against them:
1) They're trash in CQC. If a Shotgun Run n' Gunner gets to halitosis range, it's too late to begin charging unless s/he messed up.
2) Missing is extremely punishing due to the charge time.
3) Using the weapon significantly reduces your effective mobility; sprinting and sliding offensively are off the table, and firing from mid-air has never worked for me. They are not conducive to a Run n' Gun style.
4) They make a very distinctive sound. This tips your hand to the enemy giving them time to prepare, and when you're used to them you get a feel for exactly when they're going to fire by the sound alone.
Shooting from cover is the safest way to avoid eating hadrons. If that's not possible, jumping to the side just before a Fusion Rifle fires is an effective way to avoid death. If you're close enough, you can jump over their heads and rain buckshot on them from above. If you're really familiar with them, you can Slide right under their fire and kill them. The recoil will divert most of the shot above you, unless they were aiming for your legs. I've done it a few times, and nothing is more satisfying. Whatever you do, don't be an easy target; don't run in straight lines, and don't get greedy with your shots. Use grenades to reduce your Time to Kill. Lastly, your load-out can't answer every encounter. Know your strengths and capitalize on them. Accept your weakness, and avoid having them exploited.
The problem, for me at least, is in the map with hallways, if a fusion rifle catches you in a hallway no matter how close you are or what gun you have you are dead. Other than that I think they're fine.