I'm going to come off as a bit overly negative here, but I truly believe what I say. The simple answer to your question, IMO, is that Bungie didn't put much though into it. Like many of the peripheral systems in Destiny, the gunsmith is nothing more than yet another repetitive activity to keep us grinding yet another rep meter in the hopes of yet more RNG-based rewards.

I bet there was a small amount of conversation within Bungie at some point where a couple designers said "we don't want to make the Gunsmith weapons OP, right?" "no, just make them all crappy to be safe".

I'd have thought they were made crappy on purpose. It is supposed to get you to go into usual activities with a gun that is much worse than you'd usually have, and that has no interesting perks whatsoever, to force you to compensate by just being better at the basic gameplay loop. When your gun refunds missed shots, chains lightning damage, gives you bonus ammo, and all manner of other crazy things, it means you don't necessarily have to be 100% on the ball with the basics of dodging and shooting. The crappy gunsmith guns don't do that, have low light levels and bad stats. In return for making your ordinary activities more difficult, it rewards you with reputation that allows you to order more guns.

On balance I think you're expecting too much at this point to see the in-game reasons for things match the design parameters. They pretty much don't anywhere else, why would it apply to the gunsmith?

I've always thought that a "gun" that just teleported small pieces of metal into people's heads would be pretty awesome in a sci-fi movie or game. Lock on target, drop a penny in the hopper, and they fall over dead. You could even teleport air in there and give them a massive stroke. Or (slightly messier) reverse the weapon and remove chunks of their grey matter.

Teleport In: Live shark.

Teleport Out: Innards.

It was exactly this testing that led me to the HAKKE D series of weapons. Ultimately I found the Arminius-D to be my favorite gun. Co-incidentally it was so powerful they had to nerf it (not enough to make me switch though).

I continue to test the gunsmith's weapons. Bungie seems to make changes in the line up. I like being reminded why I do or don't like a weapon's characteristics.

I'd actually like to see weapon perks that are great, but come with specific drawbacks. Introduce a nice risk/reward mechanic. I feel like they need to revamp perks and make them more interesting or just remove them. As it is, I can barely tell the difference when I switch up the stat boosting perks. Those are boring, in my opinion.

Of course these ideas would be problematic for PvP, but what else is new ;)

Ding Ding.

More reason to completely separate the weapon set of PvE and PvP.

All that said, I think there is plenty of potential in there somewhere... the Gunsmith could certainly be worked into the game in interesting ways in the future. For example, what if the prototype weapons functioned like true prototypes: Awesome and creative new features, but they don't always work quite right. A rocket launcher with a DEVASTATING payload, but once in a while a projectile will fail to detonate. A new machine gun that has a super-fast reload, except that it jams every now and then.

I'm all for the Gunsmith prototypes being creative and with major drawbacks that allow them to be fun and maybe even a bit OP at times, but misfiring rockets and jamming weapons sounds absolutely terrible and unfun. If it happened too often, it'd be really annoying and not fun. If it didn't happen often enough, there wouldn't be a point to it happening at all. And let's not forget that most people would just be confused that their gun isn't working.

The Gunsmith should be revamped for sure, with crazy weapons. But misfiring, jamming weapons shouldn't even be on the table in my opinion.

Those specific "drawbacks" might be bad examples, but I do think it would be cool to have gunsmith prototypes that "go wrong" in some hilarious way. These aren't weapons that we earn or are invested in... We pick them up, take them out on patrol for 15 minutes to complete a bounty, then scrap them. There's room for Bungie to have some silly fun there in ways they don't with the rest of the game. Of course these ideas would be problematic for PvP, but what else is new ;)

All that said, I think there is plenty of potential in there somewhere... the Gunsmith could certainly be worked into the game in interesting ways in the future. For example, what if the prototype weapons functioned like true prototypes: Awesome and creative new features, but they don't always work quite right. A rocket launcher with a DEVASTATING payload, but once in a while a projectile will fail to detonate. A new machine gun that has a super-fast reload, except that it jams every now and then.

I'm all for the Gunsmith prototypes being creative and with major drawbacks that allow them to be fun and maybe even a bit OP at times, but misfiring rockets and jamming weapons sounds absolutely terrible and unfun. If it happened too often, it'd be really annoying and not fun. If it didn't happen often enough, there wouldn't be a point to it happening at all. And let's not forget that most people would just be confused that their gun isn't working.

The Gunsmith should be revamped for sure, with crazy weapons. But misfiring, jamming weapons shouldn't even be on the table in my opinion.

The be fair, the special, class-specific guns do have the feel that I'm looking for; I just wish that the prototyping was more procedural and ongoing than the current very disappointing rep weapons.

I bet there was a small amount of conversation within Bungie at some point where a couple designers said "we don't want to make the Gunsmith weapons OP, right?" "no, just make them all crappy to be safe". They came up with a handful of test weapons (how many are there? 10? I don't actually know) and designed a small set of corresponding bounties, and threw it in the game. All of it is under-developed, makes very little sense in terms of how it fits into the fiction of the game world, and adds virtually nothing in terms of unique or rewarding gameplay experiences.

All that said, I think there is plenty of potential in there somewhere... the Gunsmith could certainly be worked into the game in interesting ways in the future. For example, what if the prototype weapons functioned like true prototypes: Awesome and creative new features, but they don't always work quite right. A rocket launcher with a DEVASTATING payload, but once in a while a projectile will fail to detonate. A new machine gun that has a super-fast reload, except that it jams every now and then.
How about new weapons that don't fit into the current archetypes? A flamethrower? A laser-gun? Grenade Launcher?

As Blackt1g3r already pointed out, these kinds of additions would require more substantial work from Bungie. It seems to me that Bungie has entered "The fans need content, lets get stuff out the door no matter how underwhelming it is!" mode. Personally, I'd much rather have longer waits between updates and get genuinely substantial stuff added to the game.

But I'm not sure how that held up past actually getting real weapons of those types -- it feels like an intro kind of thing, but they also used it for rep grinding which is not ideal.

Personally, I'd love to see the weapons actually seem like they were testing something. Either a perk that doesn't normally land on that archetype (shotguns with explosive rounds, a full auto hand cannon, or maybe a sniper rifle with a Sureshot IS instead of a scope), or something even more extreme (a shotgun with vortex, "find more special ammo", and performance bonus, as well as full auto, for example, or a bullet hose auto rifle with minimal stability that uses skip rounds and has a massive clip... Stuff like that.

When I first heard about the concept, I thought it would all be stuff like this. And the fact that you have to kill specific enemies (usually majors) just makes it feel like a total chore.

Personally, I'd love to see the weapons actually seem like they were testing something. Either a perk that doesn't normally land on that archetype (shotguns with explosive rounds, a full auto hand cannon, or maybe a sniper rifle with a Sureshot IS instead of a scope), or something even more extreme (a shotgun with vortex, "find more special ammo", and performance bonus, as well as full auto, for example, or a bullet hose auto rifle with minimal stability that uses skip rounds and has a massive clip... Stuff like that.

It would be really interesting to have prototypes with new gun features, but that would require adding new content to the game. So far, that's been more difficult than it should be for Bungie. That said, I'd really like it if the prototype weapons had interesting features that could make them very powerful, but since they are prototypes they should also have significant problems. Maybe a shotgun with firefly occasionally damages the player as much as their opponents? (Actually, that's the tradeoff ice breaker should have had. Infinite ammo, but sometimes the gun "misfires" and damages you instead or pehaps it overheats and if you don't watch your shots you'll take damage?) Perhaps a sidearm that hits targets behind your targe but is extremely unstable and has a tiny clip.