I really loved playing in the point of view of a merely normal ex-military pilot, it leaves aside the typical "chosen one" protagonist POV (or the chosen one that don't want to follow his destiny), it even leaves aside the typical new military pilot POV of the original games and personally i relate more to a civil type of character, making me more involved with the story.
The limited loadout and ships to use also makes me feel the very limited logistical background and because of that is a must to choose selectively the weapons and ships of the squadrons and give them orders in-mission accordingly, also it was a pretty good detail the fact that any additional effort in fulfilling the bonus objectives come with the prize of new ships and weapons to choose, things that are insignificant in a normal military context because your superiors gives to you new equipment without any extra effort.
I liked a lot how you sticked to the Blue Planet lore, trying to use the unused assets and respecting the timeline of the events (i loved seeing for the first time the Sanctus MK2 and the Karuna MK2 in-game) and even trying to make a parallel story without affecting the events of the main story of the universe.
The character development is good, i also liked the development of the friendships of the protagonist, those very informal conversations gives an interesting change to the strictly military chatters of the original game.
Also, i think the choice of a second person narrative after and before the missions was very good, it's sounds strange in a book novel, but in a game it's fit perfectly IMO, because actually you are the protagonist.
And while it's true that in the last missions the story turns into a guerrilla warfare and winning it or not wouldn't make any significant change in the UEF-GTVA war, the emotional attachment that i felt in that stage was so good that i also wanted revenge against DuValle at any cost, the ending was superb (maybe a slightly cliche with the speech of "your friends will be always with you", but really i couldn't have done it better by myself, so i'm not really in a position to criticize that)
Now... talking about flaws in technical details of the missions, i've noticed these:
1. In Treasure Hunt II and Evidence, the briefing music keeps playing alongside the in-mission music.
2. In Sunrise, the Akebono's engines got all destroyed when it's hit by the shuttles, but magically all re-appears when her engines are repaired, it's a purely aesthetic detail (and considering the limitations of the engine i think there is not much that can be done for a visible reparation process) but maybe it may seem more realistic if only two engines get destroyed and the other two simply get turned off (if i recall correctly this can be done via SEXP) to then turn them on when the Akebono jumps, again, it's just a aesthetic detail.
3. In all missions where the Apollos are present in a squadron, their icons don't appear in the ship/loadout selection, however i can change their loadouts but not the ships.
Anyway, none of these disrupted my gameplay, and i'm not sure if the culprit are my files for the 1st and the 3rd (i have played with the 3.8.0 release and latest bpcomplete at the moment i'm writing this)
In general i felt the missions balance good (maybe Sunrise is a slightly hard, but if that was your intention then that's ok)