I agree, we need instances that require greater teamwork, more players, that take longer to complete, that does not have a timed bonus reward, that drops better loot and also have multiple boss's in one instance.
I also think they should rework the personal reward system. Lets face it, how many maco or omega parts have you got multiple times but have never gotten that PSG or ENGINE or what ever you need, but your buddy always gets that item you need and you always get the item they need. So add a universal drop box, this would include map only items that people could need, greed or pass on. The personal reward drop should only contain level appropriate consumables, consoles, weapons or items.
Before someone says this rewards system will never work in PUGs, well a lot of things don't work in PUGs. Does not mean they are broken or useless.