They're just duplicates for selling as far as I can tell. Yes, it's a bad system.
I personally like it a lot, it's very simple and effective, you can just focus on upgrading your prefered weapons/playstyle without any limitations like RNG loot, you just keep playing the game in a linear fashion, progressing, and everything is open to you, instead of having to keep going back and forth and hopefully farming to get a particular gear.
If anything, I'd change it to something even simpler, like R&C system where the more you use the gun the more it leveles up it. And I feel that weapon wheel would've been a great addition as well, to change weapons on the fly instead of going into the menu and pausing the game to manually switch the weapons when needed. And maybe add weapon mods like extended mags, explosive rounds, electric/digital dmg, piercing bullets, burst/full auto fire mode etc. instead of separate weapon types.
But I agree there's a room for improvement to make the game even better than it already is. For starters, the side quests - I cannot understand why only one quest at a time can be shown on the map/radar, very often you're inside an area where you have to search for something for a side quest, but unless you select that quest as the active one you'll never know you're in that particular area already and you could've progress in a side mission while passing by.
Secondly, the side quests being locked behind the main quests/storyline is a bad idea. Now, it makes sense that a guy wants you to bring/pick up something from a certain area that is logically unavailable for you, like The Pinnacle or Stimtown, but not every single one of them god dammit... There should be small quests possible to pick up and finished right away, within the already available areas, to level up, gain cash, weapons, skills etc.
The UI and map have been talked to death already. While you get used to the UI after some time, it would be really nice to see how certain statistic affect the character, skills, augmentations etc., you never get to see what kind of stats the augmentations have, how they level up with atributes.
The map as I said before, needs to be 2D showing the current level only with stairs/elevators to other levels. I'd also like to see a custom marker, where you select a point on the map (like for searching the chests) and then you hit the Up potton amd it shows you how to get there.
As for the gameplay side, the button config isn't optimal IMO, Aug1 should've been on RB and Aug2 on LB, crouch would've been so much better on the right trigger, while Tactical gear on B button. Auto-reload would be nice too, instead of having to look up at the ammo count to know why you character suddenly stopped shooting... And auto-fire for every gun, I'm surprised pump-action shottys have it but single/burst weapons don't, why? It makes them kind of boring, exhausting to use in the longer term.
Overall, I feel the game just as Titanfall 1 was, is a fucking awesome base that can evolve into something even much better, it just needs more of the same really, more weapons, more levels, more quests, more enemies/bosses, with small improvements here and there, that's really it. So let's hope that unlike Titanfall 2, Neon Giant won't try to completely reinvent the wheel and ruin what the game has brought into the table. My biggest concern is they'll listen to all those garbage journos and remove everything that makes the game unique, only to ironically get lower review scores for the game losing its identity.