So, I played through Fire Emblem: Awakening a few times, and now I've moved on to Etrian Odyssey IV.
In the past, I've always liked the Etrian Odyssey games better than the Fire Emblem games, but in this case it's the opposite. The Fire Emblem game still calls to me.
Obviously, this is largely the fact that this Fire Emblem game is probably the best Fire Emblem game in the series... but, on the other hand, it looks like this Etrian Odyssey game is probably quite good in its series, too. A lot of the boring stuff has been cut out and some interesting new stuff has been added in. Still, it feels... less interesting.
I think it's because Fire Emblem: Awakening has superb flow, while Etrian Odyssey actually has terrible flow.
What do I mean?
In Fire Emblem: Awakening, you always have one more thing that pops up. When you complete a battle, there's always another detail that appears. Did someone's vignettes advance? Does someone need a class change? Is there a new random monster or shop available? Did someone not quite make the vignette or level requirement you were aiming for, and therefore you just need a little more fight?
This gives the player a continuous stream of engagement without loading him down with easily-forgotten state variables. That means you can play and play and stop and pick it back up and play... The battles themselves are pretty small, so none of them get complex enough to make you completely lose track if you stop playing in the middle of a battle.
On the other hand, Etrian Odyssey IV doesn't have the strong flow. While each individual piece is entertaining enough, they don't chain together very well and they are high on state variables. So if you go exploring in your airship, it's fun... but then you're done and there's really no pull to the next thing. There's a payoff, but no clear next thing. Similarly, they've started to use mini-dungeons. When you finish with a mini-dungeon, there's no clear next thing.
Worse is that even in the full-sized dungeons, exploration is complex enough that you can easily forget where you were exploring. Unless you keep a very careful map (drawing walls), you're likely to forget which areas have unexplored branches. While there's always more to explore, the pull is state-heavy and, if you stop, when you come back you'll have completely lost track.
This combines the worst engagement practices. Poor segue for most parts of the game, and state-heavy flow for the rest of the game.
How would I try to improve the flow if I was designing Etrian Odyssey?
First off, I would make the leveling up and equipment management even chunkier and more modular, but only allow players to level up when they returned to town. So when you finished (airshipping/dungeoncrawling) there would be the urge to do that little bit of advancing. I would also include advancing/random character interactions, so that each time you return to town there are people waiting there with new things to say and ask for. These would combine to give the city a bit of gameplay that can "pump" the player from one exploration segment to another without being so state-heavy things get lost or confused.
Second off, I would make the airship thing different. Exploring the map is fun, but collecting food and selling it isn't. There's not really anything interesting about the airship aside from creating the base map, so I would want to make something interesting about it. Maybe your team doesn't fight airship-grade monsters as an adventuring team, but instead each class has different crew abilities on the airship, and you fight enemies in a customizable airship instead of as an adventuring team. Similarly, some sort of airship upgrade/maintenance system for when you land would create a good segue off of the flight mechanics.
Lastly, I would change the auto-map so that when you explore, it automatically paints walls. This way you won't forget where there aren't any walls.
Obviously, this is just a thought exercise. But I really do think that the reason I like Fire Emblem: Awakening more than Etrian Odyssey IV boils down to how well they keep the flow.