Just for fun, my thoughts...
25 Man LFR is important and should be maintained. It is fun for a lot of people, but there needs to be extra incentive to keep geared raiders doing it week in and week out.
Flex should replace normal mode, and in doing so, personal loot should be dropped in favor of the following: the number of pieces dropping scaled to the number of players in your raid. (10 = 2, 15 = 3, 20 = 4, 25 = 5)
The bonus rolls through coins are awesome and should be maintained for LFR and Flex.
Heroic difficulty should remain 10 and 25 separated.
More 5 man dungeons should be opened regularly throughout the expansion cycle. The gear that drops however should remain at "Blue" level even as dungeons open late in an expansion.
They should expand on 5 man dungeons however, and offer a real Heroic Difficulty, which would be akin to challenge modes in complexity and gear scaling. However, I believe that the timing mechanic in Challenge Modes should be removed, it's just kind of silly. Difficult 5 man bosses with very tightly tuned enrage timers (heroic scenario tech - per boss timers??) would be a better fix.
I think the current scenario system is great. I think Heroic Scenarios should be added to the group finder though, they aren't hard enough to justify forming your own groups and that is totally OK.
I think the Timeless Isle is pretty good. I like the rare spawns, though perhaps they could be randomized. More random events would be cool (a la Guild Wars 2)
I'm really glad endless dailies are no longer considered a "good" idea. Let us grind as little, or as much as we want.
I really really liked this expansion's approach to the Legendary Quest. A bit of a let down that there is no weapon though. I don't think it would have been too difficult to add a weapon .... Just think Battered Hilt -> Quel'dalar type implementation.
I don't really have any thoughts on PvP since I haven't really pvped since 5.2 /shrug
If anyone else has any constructive ideas or feedback let's get the ball rolling.