Tl;dr we don't need anything that takes that long to explain.
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Is it that complicated? Or is just the current system that is over simplistic?
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The current "system" is a lack of a system. I vote for easy, obtainable, streamlined, and simple, while powerful, so people can get it together and not dwell in the tower all day doing this.
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I honestly feel that the system I described is easy: -Find the base gear you like aestheticly; -Craft the perks you like to it. Its that simple. Grinding gains a purpose. I just mention using a Workbench in the tower to give a purpose to the Gunsmith, since he is pretty lonely and this would be up is alley. But I would just as happy to use the ghost to add these perks... I love going to the tower just as much as the next guy, specially since we can't go straight from a planet to the tower (unless you make join to a player there... which is just stupid). Adding the NPC's for these purposes with some sort of quests would also give purpose to going into PvE.
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Forget using existing gear in inventory for base model, just select it at vendor. No need to provide. Also, look at your toutatis and Vanir helmets if you're a titan. There's toutatis with headset thing and without etc. lots of little variations. Be easier and better to just scroll through these and choose color too right at vendor.