Endgame in FFXIV 1.x

1. Dzamael Darkhold (instanced dungeon, eight man)
2. Cutter's Cry (instanced dungeon, eight man)
3. Aurum Vale (instanced dungeon)
4. Hamlet (instanced half-hour event, three locations)
5. Good King Moggle Mog XII (primal battlefield)
6. Ifrit (primal battlefield)
7. Garuda (primal battlefield)
8. Skirmish (instanced dungeon, four members?)
9. Nael van Darnus Hard Mode (1.x only, will not return for 2.0)

I never did Skirmish and know very little about it. My understanding is that it was a string of battles against weaker versions of bosses from other dungeons and NMs. The rewards--materia meld-able weapons--were largely underwhelming when compared against primal weapons. I haven't looked to see if they're more viable in version 2.0. I'll look into that, now that I'm curious about it.

Edit: The skirmish weapons have two material slots, and their item level is 52, which means that they can use Tier III materia. Their base damage is lower than any of the primal weapons, and their base stat bonuses don't compare to primal weapons and still won't even after melding two Tier III materias onto it. They'll be decent starter end-game weapons, and a step up from most anything crafted, but you're probably better off chasing primal weapons at level 50.

In addition, the relic weapons quest invited you to repeat certain endgame content basically on hard-mode. It required speed runs of Hamlet, Cutter's Cry, and Aurum Vale as well as defeating Garuda (difficult) and Ifrit Extreme (really difficult).

2.0 will see all of the above (excepting Nael van Darnus hard mode, which was story-related) returning, if not in the exact form. We can expect that the dungeons will probably be re-designed, and they've said that Hamlet will be a large-scale FATE event rather an instanced half-hour event, which makes sense as it was basically a smaller-scale Besieged (if you're familiar with FFXI) which required crafters and gatherers to succeed. There will also be new additions to endgame at launch:

1. Titan (primal battlefield)
2. The Crystal Tower (instanced dungeon, 24-man)
3. The Great Labyrinth of Bahamut (instanced dungeon, 24-man)
4. Wandering Primals
5. High-Level FATEs

The wandering primals will be the same primals from the eight-man battlefields except scaled up in power. When defeated (requiring an entire free company), that free company gains the ability to summon the defeated primal once. The entire world's weather will change to reflect that the primal has been summoned (presumably fire in the sky kind of thing when they summon Ifrit), and then the primal will be released into the world again for others to defeat. This is probably the closest thing to HNMs that FFXIV will have. As for the high-level FATEs, we don't know much about them except that they will be around.

In the future, they'll be adding more primals. Confirmed as part of the lore already are Ramuh, Shiva, and Leviathan. There is no word yet on when they will be added, but probably later and probably one at a time. I'm sure that we can eventually expect primals beyond that. I'm sure that the first expansion (planned for a year after launch, I believe) will bring more dungeons and battlefields, but they expect major content updates every two months, some of which will likely bring new endgame events as well.

As for free companies, you don't need one at all, although I imagine that the Crystal Tower and The Great Labyrinth of Bahamut will be very difficult to tackle through the Duty Finder. Additionally, endgame events will have trophies that can be displayed in Housing (which is, at launch at least, exclusive to Free Companies). Defeat Ifrit? Get an item (his horns) which can be crafted into a trophy to display above your mantle. Also, because free companies are the only way to get player housing until personal housing is later added through a patch, being part of a company will be the only way to get the bonuses from housing.

Edit: I'd also like to clarify that the level 35 cap is only for beta, and I believe that it will be lifted for the fourth phase (which is the open beta).