I just have a few ideas kicking around in my head that I thought I would throw out there. Some of them are tiny changes that I would beleive would be easily implemented, others are changes that would require a lot of time, and are more or less feedback for future expansions and titles.

The flavor of upgrading exotics

I'm not going to get into the player progression or investment system here. This is a minor nitpick. Xur's selection of upgrades is labeled under "Purchase Upgraded Exotics" I really really don't like the flavor of that. It makes it seem like he has a storeroom of a better version of my beloved Thunderlord. I suggest changing the title of that section of his store to something like "Reforge Exotic items" or "Ascend Exotic Items" just something a bit more flavorful and less mercantile.

Lack of endgame for PvP

Now I'm sure people will argue that Iron Banner is the endgame for PvP but I disagree. Iron Banner is an event. PVE has story missions, strikes, endgame raid content, and a limited time event in the form of the Queen's event. Crucible just has Crucible and IB. I have a few options for high level pvp content that also rewards for doing it.

First, is a ranked matchmaking with publicly viewable ELO matchmaking and seasons. This would have a high light level requirement for an even playing field. It would also be able to use the existing clan system for Team rankings.

The next idea is faction wars, which should be self explanitory.

Third is world pvp, which im not sure how easy it would be to implement and it would clash with the flavor of destiny.

Either way, high level pvp gear I think is a must to help incentivize this aspect of the game.
Useless NPCs

OK useless may be a bit too harsh, but Banshee and Holiday both aren't worth visiting daily for most players.

For Holiday I think something like Exotic bounties but with cool rare ships as a reward would be a nice way to make her more useful, as well as adding flavor to the world. The quest system that Eris has is a good example of how I think we can make Holiday and ships and sparrows stand out.

Banshee simply needs some sort of legendary inventory or something. I also think as a long term goal letting him reforge things would be nice. Or maybe some sort of weapon customization for rares? Building a custom handcannon for PVP would be a fun thing I think.