You can't just wholesale cut out the Company of Heroes arc. It introduces Riol, one of the more prominent Scion NPCs, and finding Drex (the Imperial soldier stranded outside of Wineport) and seeing that he was a perfectly normal guy just like everyone else really helped humanized the Empire, especially when even still, after all this time, the Empire is still portrayed as an overall one note cartoon evil empire. Plus, Shamani was one of the most memorable ARR NPCs as well.
In fact, now that I think about it, you can't cut out a lot of sections either because those seemingly minor NPCs come back to be pretty major characters in the plot, such as Laurentius, Yuyuhase, Alliane, Meffrid, and so on.
The Garuda arc could be heavily edited down, the only thing that really needs to stay is Cid's explanation of how to breach the barrier, as that comes back as a plot point later. Otherwise, the whole fetch questchain could be eliminated in it's entirety. "Go to the guild and ask if they have a corrupt wind crystal". "Sorry, we don't have corrupted wind crystal, go to this guy out in Drystone and ask him". "Oh hey, go get this thing from me over there". "Thanks for the thing! Oh wait, you're looking for a corrupted crystal? Well this thing isn't it. Go over there and get one!". "Oh, you came back? ... Oh, you wanted a corrupted WIND crystal! Well you ACTUALLY need to go over there to get one!"... etc. I'm sure the Grand Companies have at least one so it'd be as simple as having Cid ask a Twin Adders NPC to go get one from the quartermaster. Boom, done. It'd retain the sense of urgency that Garuda threat poses.
The post 2.0 Primal segments could definitely be edited down so that they aren't as intrusive. No, I don't need to spend an hour running through the Sylphlands chasing an NPC whilst pulling aggro from everything we pass by. Just let me get straight to the comedy bits with the Archons and meet Ramuh. No, I don't need to spend an hour running back and forth through Sahagin territory whilst pulling aggro from everything we pass by. Just let us find the priest, raft the two ships together and fight Leviathan.