Hmmm, really interesting way you describe it. I'd actually very much like to have seen this in the game, though I agree with Avi448 in that I still enjoyed Awakening, but the execution was the real problem.
Personally, I wouldn't go so far as to make as many changes to the overall story, as much as just small restructuring and more details to flesh it out more.
Here's how I would improve it, arc by arc:
Plegian arc
I really think Emmeryn should have been fleshed out more, and I love your idea of making her a playable unit. Give us more background. It serves the world's lore much more to say "Back when Lord ... (Chrom's father) did this campaign, Plegia suffered. Gangrel wants to get revenge on us because of Lord ...'s atrocities. It's better to give names and actual events and descriptions rather than vague "Chrom's father hurt Plegia." I honestly think the Plegia arc is pretty much good to go. Again, just give Emmeryn more development to make her death more impactful, and give more lore to the previous events in Ylisse before the war with Plegia.
Valm arc:
Show Valm invade Archanean continent. Not just the Valmese arrival in the docks scene, I want a cutscene showing part of the battle, and a better defense mission. Make the first part of the Valmese mission playable in Regna Ferox. Ex) Chrom/Shepherds arrive to Castle Ferox at the heat of the battle, and have to fight through an ongoing battle between Valmese and NPC Feroxians. At the end of this mission, there are Basilio and Flavia engaged with a commander, and if you don't make it in time, one of them dies at the end of the mission. Make this force a threat to us. Spread out a few more Grimleal missions here and there. Kinda like the one with Gregor/Nowi, but in the middle of Valm. We are told that Walhart wants to unite the world to stop the Grimleal, but really why does he care? Let us see Grimleal presence in Valm, and maybe even have a small alliance mission with the Valmese for a mission. More of Walhart: we only see him a few times 1) when he "kills" Basilio, and 2) final battle with him. Let him appear kinda like Excellus does a few times, to taunt the Shepherds or explain his motives as he retreats. Final battle should be to storm his castle, and then after you defeat Walhart, he explains his true motives at last, and then dies. After he dies, Grimleal/Validar appear and use Valm's temporary vulnerability to seize control. Valm was the weakest arc, and more Grimleal presence is the key here. That and more Walhart to really flesh this out and give us a sense of purpose in this war.
Grima arc (I actually like this arc a lot, but to really benefit it, here's what I think should be done)
Robin and Chrom confront Validar and Validar steals the Fire Emblem. Enter Lucina HERE instead, where she helps the Shepherds escape and saves Chrom from Robin. She explains the state of the future and after this point, the kids become available. Make this arc twice as long as it is. As it stands, it's the shortest arc of the game, but it's the main story of the game in this arc. Making it longer here, and making this the point where kids become available makes the kid's presence have more purpose, rather than just being "hey we wanna help you out and stuff. Oh yeah we gotta fight Grima, but first let's do this Valm thing cause Grima's not THAT important right now". Expand on Validar. Make him slightly less "I'm evil cause evil" and connect Grima's restoration to Medeus and Marth's legends. Tie this all in somehow. More on the Deadlords. Seriously, these things are so cool and are a great reference to Genealogy of the Holy War/Thracia 776. Expand on their presence, and why they hold the legendary Holy Weapons. Maybe these Deadlords resurrect with the Fire Emblem, and Validar uses them to try to capture Robin to fully resurrect Grima or something. Maybe these Deadlords act as the main generals for each of the missions in this arc until the end. Seriously, these would make for a more mythical, and interesting fight. After beating the Deadlords, Validar finally does his control Robin thing, until Robin, after having spoken to Lucina, figures a strategy to prevent himself from being controlled. Give Lucina more development by making her talk to Robin between missions for a few cutscenes to figure out the whole Grima thing. Let the plot continue as normal now, as the rest is fine.
Again, I don't think we need to completely change the structure of the story, rather than just expand on things more and change up a few tiny details to flesh the world out and give more purpose. This is just my idea.
Hmmm, really interesting way you describe it. I'd actually very much like to have seen this in the game, though I agree with Avi448 in that I still enjoyed Awakening, but the execution was the real problem. Personally, I wouldn't go so far as to make as many changes to the overall story, as much as just small restructuring and more details to flesh it out more. Here's how I would improve it, arc by arc: Plegian arc I really think Emmeryn should have been fleshed out more, and I love your idea of making her a playable unit. Give us more background. It serves the world's lore much more to say "Back when Lord ... (Chrom's father) did this campaign, Plegia suffered. Gangrel wants to get revenge on us because of Lord ...'s atrocities. It's better to give names and actual events and descriptions rather than vague "Chrom's father hurt Plegia." I honestly think the Plegia arc is pretty much good to go. Again, just give Emmeryn more development to make her death more impactful, and give more lore to the previous events in Ylisse before the war with Plegia. Valm arc: Show Valm invade Archanean continent. Not just the Valmese arrival in the docks scene, I want a cutscene showing part of the battle, and a better defense mission. Make the first part of the Valmese mission playable in Regna Ferox. Ex) Chrom/Shepherds arrive to Castle Ferox at the heat of the battle, and have to fight through an ongoing battle between Valmese and NPC Feroxians. At the end of this mission, there are Basilio and Flavia engaged with a commander, and if you don't make it in time, one of them dies at the end of the mission. Make this force a threat to us. Spread out a few more Grimleal missions here and there. Kinda like the one with Gregor/Nowi, but in the middle of Valm. We are told that Walhart wants to unite the world to stop the Grimleal, but really why does he care? Let us see Grimleal presence in Valm, and maybe even have a small alliance mission with the Valmese for a mission. More of Walhart: we only see him a few times 1) when he "kills" Basilio, and 2) final battle with him. Let him appear kinda like Excellus does a few times, to taunt the Shepherds or explain his motives as he retreats. Final battle should be to storm his castle, and then after you defeat Walhart, he explains his true motives at last, and then dies. After he dies, Grimleal/Validar appear and use Valm's temporary vulnerability to seize control. Valm was the weakest arc, and more Grimleal presence is the key here. That and more Walhart to really flesh this out and give us a sense of purpose in this war. Grima arc (I actually like this arc a lot, but to really benefit it, here's what I think should be done) Robin and Chrom confront Validar and Validar steals the Fire Emblem. Enter Lucina HERE instead, where she helps the Shepherds escape and saves Chrom from Robin. She explains the state of the future and after this point, the kids become available. Make this arc twice as long as it is. As it stands, it's the shortest arc of the game, but it's the main story of the game in this arc. Making it longer here, and making this the point where kids become available makes the kid's presence have more purpose, rather than just being "hey we wanna help you out and stuff. Oh yeah we gotta fight Grima, but first let's do this Valm thing cause Grima's not THAT important right now". Expand on Validar. Make him slightly less "I'm evil cause evil" and connect Grima's restoration to Medeus and Marth's legends. Tie this all in somehow. More on the Deadlords. Seriously, these things are so cool and are a great reference to Genealogy of the Holy War/Thracia 776. Expand on their presence, and why they hold the legendary Holy Weapons. Maybe these Deadlords resurrect with the Fire Emblem, and Validar uses them to try to capture Robin to fully resurrect Grima or something. Maybe these Deadlords act as the main generals for each of the missions in this arc until the end. Seriously, these would make for a more mythical, and interesting fight. After beating the Deadlords, Validar finally does his control Robin thing, until Robin, after having spoken to Lucina, figures a strategy to prevent himself from being controlled. Give Lucina more development by making her talk to Robin between missions for a few cutscenes to figure out the whole Grima thing. Let the plot continue as normal now, as the rest is fine. Again, I don't think we need to completely change the structure of the story, rather than just expand on things more and change up a few tiny details to flesh the world out and give more purpose. This is just my idea.