From what I've heard from friends you might unlock a shader or two in the first couple of levels, or you might get your first shader much later (e.g. level 100). Even though I've started playing Destiny since launch, I haven't really bothered with the factions up until a couple of weeks ago. I have seen some faction items drop (armor, weapons) but sometimes you'll just get rewarded with motes or strange coins.
Having the faction handlers sell these shaders wouldn't do any real harm, after all Eris Morn, Lord Saladin, Petra Venj and Variks will sell you shaders after having achieved a certain level. So why not let faction handlers sell theirs as well?
With that being said. I like the idea of having the three factions matter more, I was in fact discussing this very idea with some friends a couple of nights ago. I suggested that by wearing a faction class item you'd get faction-specific missions in patrol and getting faction reputation for doing activities whilst wearing faction class items such as the Vault of Glass, Crota's End, etc. which count towards the total reputation earned for said factions. This mechanic could coexist in tandem with your ideas to cater to the PvE crowd.
To make a long story short, the factions are interesting. Bungie should do more with these.
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This needed a bump, also mentioned your thread in the community wish list thread. Keep fighting the good fight.