I can only comment on Frontlines, as that's what my "end-game" consists mainly of since hitting level 50 last week.
First off, despite Twin Adder's abysmal lack of coordination here on the Jenova server, I still very much enjoy Frontlines. I feel the rewards are adequate for the most part, however I believe that the amount of Mythology and Soldiery should be reduced depending on what place you're in. For instance, 1st gets the normal 50 Myth and 25 Soldiery, 2nd gets 40 and 20, while 3rd receives 30 and 15. Something like that. Here on Jenova, we have several players who queue for FL, and then "AFK" in a fashion. They'll move within the two minute window, preventing them from getting kicked out. Some, even boldly throw insults at the teams actively engaged, while still standing in the same place they spawn; again, to prevent being auto-kicked. I believe this will deter those that are there for the free Myth/Soldiery, and opt to either actively compete, or do something else.
On the Morale issue, I believe Frontlines should be an area where Morale matters. I admit, there will be some gear discrepancy between those with, and without PvP gear, I look at the nature of Frontlines in general and find that the natural "zerg-y" nature of the game will help alleviate this issue should a coordinated team in PvP gear decide to camp an Outpost. For instance, should an opposing team in PvP gear take Manors, team C and part of team B could opt to zerg them, or run splits to other outpost that are defended by players in some, or no PvP gear. And if they do choose to tackle them head-on, I think this would promote a little more thinking regarding priority targets, and more intelligent use of their skills. The excuse of not having PvP gear seems to be a non-issue in my opinion. If I'm not mistaken, there's a set you can buy rather cheaply off the Market Place. Or better yet ( assuming it's not already done and I've missed it ), the developers could supply everyone ( through a quest no less ) with a basic set so that they're not completely helpless if they're brand new players. The amount of Wolf Marks one earns is enough to get your ilvl70 set rather quickly whether you place first, second, or third.
Rewards: I think the actual rewards of Frontlines are alright, but would like to see them adjusted. I don't however, think that about Wolf Marks. If PvP is to last in this game, and keep players interested in it, they need to add more things to purchase with Wolf Marks. Gear and Materia aside, it's pretty pointless. That's not good at all. Not for those that are dedicated to PvP, or those that are thinking about giving it a shot. Yes, there are those that PvP because it's PvP, but those people are far, far less than those that need something shiny to go after. I'm a mix between those two extremes, and as I do love to PvP, I'd like to be able to say I got this, or that thing from my efforts. With that said, I think there should be mini's, mounts, a few more titles, armors/glamours etc. things like that. This is doubly so in Wolve's Den. I think the rewards there need to outweigh those that may or may not get implemented in Frontlines as WD from what I've seen thus far, and from the general consensus here, and in-game, is dead. That's an issue that's not relevant, but should still be stated.
Just my two cents.