1. You cannot put something as essential as flying behind a skill check. If you do this you take many people out of the game completely because they cannot play as everyone else.
2. Then they have to timegate it. Which is even a bigger problem for many. I would like it. Story quests over 2 month. But in the end this would not matter a bit as everyone would get it at the same time so why have rep anyway at that point? The other way you decide how fast you get it.
3.That sounds ok. But here you will get complaints from the (according to the forums here) considerable playerbase who do not interact with players in any way... because they don't want to... in an MMO... yeah i don't get it either. But this point sounds interesting.
You will never get rid of dailys and stuff like this in MMORPGs for the simple reason, that they need you to play the game as long as possible. That is the whole system of EVERY MMORPG. I don't say this is bad. This is just the way it is. You cannot make a MMORPG where you can play JUST new stuff for 3 years... there is no game that has that amount of content. Never was and probably never will. SP can do it but you play them not even close as much as MMOs. (simulations are a different thing talking about RPGs and stuff like this with a story)