Ironically, we've met a lot of them already. We've certainly met the most influential engineers Garlemald has. Cid and Nero came up with a lot of the airship and reaper technology when they were both at the Magitek Academy together. It's entirely possible that the flagship and all other Garlean military airships we see were designed by them. However, Cid defected after one of his father's experiments killed him. Nero was part of the Legion that went (and largely stayed) AWoL. Neither of them have a lot of reason (or desire) to go back to working for Garlemald. That would also go to a sizable portion of the Ironworks engineers. Many of them are originally from Garlemald and wanted out of Garlemald so they could decide what they wanted to work on instead of the government picking for them.
Apparently, the Battle of Silvertear Skies did... something. Whatever that that something was it stopped the XIVth Legion in it's tracks and prevented them from going into Eorzea for the next fifteen odd years. What that "something" is, we don't know. We do know it has something to do with Silvertear Lake though. That said, the only reason why we know any of that is because of Koji telling us that's why the XIVth Legion didn't resume invading Eorzea until Nael was handed the Metor project.1. If their base was still operational, why didn't they keep sending fleets of airships against us? (though I vaguely remember this answered somewhere before.)
You see this happening in 4.1 when the Resistance members are going over the place Aulus was doing his research on the Resonant. You also see it in the very first MSQ quest of StB when you go to Castrum Orines, a Castrum the Alliance has occupied. Other examples would be Castellum Velodyna when it's and Castrum Abania and even Ala Mhigo itself.2. When we "liberated" the place, shouldn't we have captured lots of equipment and personnel if it was indeed one of their supply fortresses? Why wasn't there more explicit story/plot on this aspect?
For an MMO, FFXIV is very heavily story focused. In fact, many of the people who play FFXIV only for the gameplay complain about a story being involved in everything. If you haven't already, I highly suggest getting the lore books. Those have tones of story in them, a lot of which has never and probably will never make it into the game because of the limits inherent in a game's medium as opposed to a book's.3. I know i will never be as imaginative as the devs, but please consider some of the ideas here, and please make FFXIV focused on story more.