Main story stuff that might happen later on

- Space Travel to the Moon. (FF4 callback.)
- Travel to Garlean Empire on a Doom Train. (5.0 content)
- Fighting Omega Weapon in AlaMingo at the end of 4.0. (One of the Lalafell characters around Uldah's storyline in 2.3-3.0 I think wants his throne back in AlaMingo.)
- Fighting Necron (God of Death)/Zodiark. (One of the trials in 2.4 has a statue of the final boss Necron from FF9 in it. Might be this games Zodiark.)
- Fighting Shinryu at the end of 3.5. (Collection of Dragon eyes used to summon Shinryu)
- Fighting the Moon's Dark Crystal. (End of 2.0 we seen a dark crystal.)
- Reviving Lahabrea at the end of 3.4/3.5. with one of the eyes collected from Nidhogg used to defeat him at the end of 3.0.
- Underwater zones in 4.0. (Sea of Ash/Jade, Eastern Oceans around AlaMingo)
- Getting on the Garlean Airship dungeon in patch 3.5.
- Getting access to Castrum Oriens in 4.0.

Okay I'll bite... (spoilered where appropriate)

1. Highly likely, given what we now know about Zodiark... being banished to the primary moon and everything. But it remains to be seen how we actually achieve this.
2. All but confirmed eventually, although I doubt somehow that we'll be taking a train to it (One would think an airship would be more appropriate). But who knows, maybe Ilsabard has an efficient rail network...
3. Almost impossible - it was mentioned Omega Weapon was still buried underneath the Carteneau Flats (which is the whole reason Frontline is being waged). Really though the only one who was really after it was Teledji and... well... given the fact he's now... kinda dead and gone... it means digging up and restoring Omega Weapon effectively died with him (not to mention if it's anything like Ultima Weapon it would not have been operational and would have required extensive know-how to bring up back online, something Teldji did not have).
4. Again unlikely - the effigy in the Chrysalis was revealed in the artbook to be just that, an effigy. Considering the artbook also mentioned the Chrysalis was a pocket dimension formed from the thoughts of the Ascians, the effigy was probably merely a symbol of Zodiark without actually being Zodiark (again if SE really were planning that they would have used it by now).
5. It's not confirmed but considering two of the seven members of the 'First Brood' are currently unnamed and unaccounted for, I would not be surprised if Shinryu is one of them. But again, SE will doubtless have this all planned in advance.
6. The jury is still out on exactly what that dark crystal was in that Echo vision. Whether it's meant to represent Zodiark, a corrupted Hydaelyn, or something else, remains to be seen. Either way, I think SE would probably have Zodiark being in the form of not a crystal, but a god-like being... as the Ascians are fancy like that.
7. Lahabrea is dead and buried... he was turned into aether and consumed by Thordan's Primal form to sustain himself, exactly like what Leviathan did with the Sahagin Elder way back in the 2.2 patch. Thordan himself all but states this in that scene that "Gods feed upon aether" and that "Ascian souls are no exception" - he turned Lahabrea into aether by slashing him with Ascalon, and then consumed him. He is not trapped in Nidhogg's eye, he was turned into an aetheric snack for Thordan's Primal form. Lahabrea is gone for good I'm afraid.
8. To be honest, I'd rather they didn't put swimming in, as it just doesn't fit the concept of a character in heavy armour exploring underwater - it would be more something that submarine exploration (like in FFVII) would be more suited for. But until we know more about this other than vague comments take my opinions with a grain of salt. :p
9. Uh, we already had a Garlean airship dungeon (Keeper of the Lake)... unless you mean the Gration. I'm not entirelly sure why we would need to go there, unless we're chasing down Regula. But that would require pretty extreme circumstances to do so.
10. I seriously doubt Castrum Oriens will now ever be accessible as it's pretty useless story wise (like all the Garlean castri in Eorzea, they're now just filled by a few remnant troops of the XIVth Legion, and post Operation Archon are pretty much superfluous to the story (why else haven't we already gone there> There is zero reason or need to do so, we have more important and pressing matters to attend to than beating up a few demoralized Garleans grunts who don't even have a CO anymore).

You should know the story better and make deeply researches before giving such speculations