Bungie definitely needs to make the resources for this upgrade system more abundant.Some ways to do this would be.
Marks should be able to be traded for materials like you said. I also think they should be able to be traded for glimmer as well as shards and energy, all four should be exchangeable. I always have marks shards and energy, and i never have glimmer or resources. That doesn't seem like an upgrade system that's thriving.
A potential drop in the nightfall should be a minimum of 80 of a resource i would way rather that than any legendary weapon , mark, shards, energy.
Dismantling an upgraded weapon should grant a quarter of the resources put into it back.
Vangaurd/ Crucible/Faction Rewards should be able to drop materials. Again 40 of a resource is way more valuable then a legendary weapon or 1shard and 1 energy.
Also you should be able to get a significant amount of glimmer from bounties. I think its ridiculous you don't get paid for doing bounties , what kind of bounty hunter doesn't get paid and does his job just so the vanguard likes him a little more . That just doesn't make sense lol.
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I do like the idea of glimmer from bounties, should get paid in more than experience and rep! =)