I was picturing in my head a vanilla-WoW/Everquest-esque MMO. In the "perfect" end game I imagined it would have, world events were the new raiding. Storylines stretching from the opening levels culminated in high level zones helping one faction or the another defeat their highest-level enemies.
At level eight or so you would, say, encounter your first spider. The zone would play out for a few levels with you killing spider minions, burning webs, infiltrating their base and overhearing their war talks/stealing their maps/destroying their weapons. Later in the storyline, you'de be defending from a spidery invasion (modular, based on how many weapons you destroyed/minion you killed/etc), and by level 12, you would be killing that zone's non-instanced boss. When he's dead, you'de go on a few more recon missions to discover who the real spider force is, and the instance of the zone would unlock. The level of the instance mobs would cater to the zone. If the zone finishes at 12, the mobs in the instance would be level 12-16, with most being level 14, and the boss being 15. Once you kill the instance boss, that's it for that particular zone of the spider storyline. Now you can proceed to spider zone #2.
This approach would also work very well with a level-less game design. In fact, most of it already is, given that one quest would unlock another quest, would unluck an invasion, which would then open the instance. The instance could then be run any number of times for the spider-specific loot without risking the player outleveling the next spider zone.
Creatures could also drop more realistic, non-trash loot. Spiders would drop their limbs, mandibles, eyes, webs, etc. The blacksmiths at the spider-defense town would happily craft you gear of varying quality as thanks for killing the spiders. That also solves the "NPCs are mean to me, they are charging me money even though I just saved them!" issue.
With each new zone in a storyline, the threat of the story could grow. In the second spider zone, they could start immobilizing players/NPCs and using ranged toxic spit attacks. In the third spider zone, they might be able to set web traps that'll immobilize, cause poison damage over time, and have heavy, web-enforced armor, as well as all previous abilities. By the final zone, and presumably the most bad-ass, they would have web-enforced armor, be breeding gargantuan, mindless spider-hulks, and be able to burrow under the ground and make sand traps, pulling you into their maze of underground spider-infestation.
After you've completed all the quests in the last zone of that storyline and gotten the "Collapse Spider Cave" zone ability, the "web-armor melting" weapons (storyline based, so that you'de be able to one-shot the first spider zone enemies, but still get new items when you go to fight a different enemy), you'de defeat the end boss of the spider campaign and unlock the zone instance (or possibly just allow the player to proceed to the "end game," an open-world group zone).
The final spider event could be an open zone with no player limit, or an instanced/phased world in which only your group is there. The "war effort" would be on a week lock-out, or in the case of an open world, would occur every ten days, and if completed sooner, the remaining days the zone would be quiet.
The war effort would be able to be entered even if you're alone, and some parts of it would inevitably be solo. It would not require all the players to enter at once. There would also be small group parts (5-player events, enemies tuned around two players, etc). In a war effort instance which could register 20 people to it (and thus have 20 people in it at a time), the biggest boss would be tuned to a group of 13-17 people.
Achievements would be available for those who could complete with ever-rising challenge; defeat the boss with 20 and you get the "completion" achievement. Another at 15, another at 10, another if no player is damaged by ability X, and another if you manage to defeat the boss with only one player taking damage, only one player casting healing spells, and only eight people in your group. There would also be zone wide achievements, such as to complete a war effort task in five days or less, and then a super-achievement to complete them ALL within a five day period.
There would be multiple tasks requiring different skill sets for different people.
Some tasks would require dexterity: the ability to execute a script quickly, such as jumping out of the poisoned-web before a single tick, or using an ability in time (silence a casting spell repeatedly). There will be speed tasks, where you have to do whatever they ask within a difficult timer.
Other tasks would be "hard work" parts: gather X items, kill X enemies, bring X spidercrystals one-at-a-time to spiderbase to power the spidershield. "Hard work" tasks are typically untimed quests which are often referred to as being "grindy."
There are also thinking tasks. These would be puzzles, randomized by the week, such as to plants bombs in the spider nests. All the bombs would have to go off at once, but you have to take into account things like how long it takes for you to walk from one nest to the next, or what if you get stopped and have to fight a spider. Other thinking games could include limited versions of chess, majong, and plants vs. zombies (with a random set of plants).
The intent of a 7-day timer on an instance zone, or a 10-day timer on a public zone, would be that it gives plenty of time to allow for a sufficient group to try the harder achievements on the group boss, but also allows for the 'thinking' player to come up with an optimal strategy for their non-twitch tests. Rewards will favor those who complete the harder achievements, not those who do the simple achievements fast.
Rewards would be handed out when the instance/zone resets, or if all of the war effort tasks are completed, the zone would lock right then (Victory!) and all players would receive their credits, which can be spent on loot. Credits are distributed evenly to the entire group based on how many of all the war effort tasks were completed, and how many of the achievements were gotten for that week. Therefore, you are always encouraged to complete as many of the tasks as you can in order to maximize weekly gain, encouraging players to get better at their tasks. Casual, small-group players who even collected minimum credits could spend it on more gear/abilities to increase the speed at their simple killing/gathering quests (which would then net them even more credits next time), while the group players who killed the boss with 16 players last week would be encouraged to do two of that boss this week (in different instances, if it's instanced), each with 8 players, or just to increase their rotations to do it faster next week.