I think the current system is built to encourage you to play everything in the game but it ends up just making me want to go buy stuff from the vanguard reps instead.

I like the idea of have one be purchased through crucible marks and the other Vangaurd.

Currently you earn faction rep for anything while wearing a faction class item. This is all well and good except you can only buy faction items with crucible marks.

Now while I do think in the long term factions do need to be reworked and expanded on.(patrol world pvp anyone?) there is an easy fix Bungie can do presumably in a hotfix.

I noticed that each faction has two sets of armor for each class, and 4 weapons. Currently on the vendor screen it lists the weapons and armor as crucible armor and weapons.

My suggestion is Bungie makes one of those armor sets for each class and half the weapons under a store category called Vanguard, where they are purchasable with vanguard marks. This should be an easy temporary fix as I presume factions are being expanded upon as we speak.

It clearly should be, because that is the entire reason I'm not going for any faction gear. But yes, having PvP by faction in patrol mode would be awesome. And it would be really easy for players to opt out of it by just not flying any faction colors while patrolling. One of the biggest issues I can imagine is players finding ways to abuse it (assumming it offered rewards worth abusing for). Still that one change would make the game infinitely more interesting to me.