Long-time lurker here. Lest my post look like a massive wall of negativity, let me say this right away: War in Heaven is my favorite Freespace campaign, hands down. Thank you for many hours of first-rate entertainment!
Here are some things I noticed.
The Cost of War
Once or twice, the Leeuwenhoek took 16+ minutes to reach the gate (far longer than the rest of the convoy). I haven't been able to reproduce this.
Collateral Damage
I used to lose the Akula at the start of the mission, every time. But the latest version seems to have fixed this.
Post Meridian
I used to order the Grimler team to kill each individual Maxim fighter; when I opened the mission in FRED, I realized that they're smart enough to interpret "kill one of them" as "kill all of them". It would have been nice to know this during the mission.
Ken
It took me a while to figure out that pressing "T" lets you read the containers in order. I'm not sure how this could be made more intuitive, though.
For the Wrong Reasons
Killing the hostage without aspect missiles is tricky; my primaries seem to go right through her.
Darkest Hour
I often fail the mission when the Valerie arrives, either because the Indus dies or because I die trying to disarm the Valerie. (I play on Medium.) In the dev commentary, General Battuta mentions that in early versions of the mission, the Indus was indestructible, to prevent frustration. I think this is a good idea.
The Intervention
It bothers me that I can avoid the dogfight by just flying off; few of the other missions have such an easy way out, and the dogfight is not unreasonably difficult. ("My Brother, My Enemy" is an exception with which I'm completely comfortable.) It also seems odd that Simms can hold off four fighters single-handedly. Maybe both problems can be solved by making Simms die if the player abandons her?
Aristeia
I once saw the Hydra explode (obviously a big no-no). It happened after I loaded a checkpoint.
One Perfect Moment
During the first few seconds, the player is low enough to see the jagged textures on the moon's surface. It hurt my immersion a little bit.
I once collided with a building (circular, I think?) and got flung upwards an insane distance. I guess the building's physics were weird.
Deals in Shadows
Occasionally, one of the initial Gef fighters jumps out, breaking the mission (nothing happens afterward).
Nothing Is True
It's not obvious that scanning all of the miners first is the best strategy, because the convoy's scattering is unexpected - but the second time, you know what's coming. I guess I was uncomfortable with the use of "meta-knowledge" (not that it's necessary to pass the mission).
Everything is Permitted
The subsystems are slightly tricky to scan.
One Future
Why don't the SOC fighters show up when you destroy the habitat? I would have liked to see them more often.
Her Finest Hour
It took me several playthroughs to figure out that the reinforcements jump in near your position. I don't think this detail was mentioned anywhere.
Eyes in the Storm
The refinery sometimes ends up tilted at a weird angle - because a Satis collides with it, I suspect. The Kopis once undocked very early, possibly for the same reason.
Finally, I'd like to single out "My Brother, My Enemy" for praise. Words cannot describe its awesomeness. I'd noticed the improved AI before, but this is the mission where it really blew me away. The dogfight is fun, challenging, and a little bit different every time.
