My current playthrough has petered out due to the BOS Siege bugs (I'm still on 2.47.6, no worries about bug reports) so before I upgrade to 2.47.8 or 2.47.9 I'll record my current thoughts:
The Den is really great and I only experienced a few crashes while there, so it might not be universal. I really like the Metzger talking head for 2.47.6, I assume it'll have been replaced by a head from Goat_Boy in the future though. I don't necessarily agree with the layout of minor locations surrounding the Den; the truck crash is referenced in dialog at Broken Hills as being located to the south of that town, so I would either update the dialog or move the zone. I'm guessing the former is simpler.
Modoc is great, no complaints here.
I was not able to unlock the quest to discover the Primitive Tribe's old grounds (I believe F12SE refers to this location as "Shumble"). Would like to see this available if possible since I love exploring on the world map. Another question: does the Arroyo-Umbra marriage have an impact on the ending slides? Should there be a literal political marriage, i.e. the Chosen One has to marry Sulik's brother/sister or the son/daughter of the Elder to seal the tribal alliance?
Vault City's security quests have a few bugs that I believe have been fixed. The dialog for starting the Broken Hills scout mission was unavailable, but the quest was still assigned to me. Unfortunately, the quest to deliver Moore's briefcase seems bugged; there were no circumstances in which I could get Bishop to not be aggro upon my arrival in New Reno. Also, when delivering guns to the village, they did not take the guns from my inventory.
It is not well-broadcasted that the molerat in Gecko controls the molerats at the village. Also, as a matter of taste: most people hate talking albino molerats. Would you consider changing these critters to another type? I'm sure we could find a satisfying alternative.
Also worth pointing out that the Ghost Farm's inhabitants also keep domestic molerats. I would consider linking the village to them instead of the talking molerat if possible.
The Abbey and the Monastery is another matter of taste I would like to see changed. Since nobody (that I found) reveals the location of the Monastery and the map is in my opinion of lesser quality than the one from the RPU, I personally think it would be best to integrate the Monastery's quests into the Abbey and remove the Monastery entirely. The quests could unlock after completing the EPA botany data quest, since the Monastery's quests are along the same lines of espionage/information scraping.
I wouldn't want to necessarily trash the Monastery map, though. Could it be added as another zone to the Abbey location, as a combat arena or quest area to recover material from the Order of Leibowitz's older hideout?
Not to recommend deleting one version of the Abbey and introducing another, but I did discover another take on the cut Abbey content that drags the location into conflict with the BOS. Since the BOS is present in the Megamod, perhaps you could integrate this take somehow?
https://jackburkhardt.com/projects/abbey/
Ghost Town was scant on information. My headcanon is that the pistol and armor belonged to the BOS Paladin Ulysses Grant from Fallout: Sonora. Nice little zone, would have added something more aggressive than rats as enemies. Wasps? Roaches? Scolopendra?
The Redding quest to recover the man's son from the ruined city was not able to be completed. This may have been corrected in newer versions, not sure.
You probably already know about the Broken Hills mine bug.
Vault 23 doesn't work for me. Discovering it after Mariposa, my character has battled plenty of rats. Vault 14 is the superior custom Vault; I think the two locations should be combined and placed at Vault 23's present location north of Mariposa. The giant rat lair should link up to Vault 14's level 3 and be a quest given out by one of the characters there. I also don't know what frames are being used by the giant rat, but they look odd. I would just use the albino molerat frames.
The random encounter for getting into Vault 14 also never triggered; I think using the hermit from Vault 23 to give out the keycard would be best. If you move Vault 14 to Vault 23's current location, I'd also recommend renaming it to Vault 17 as yet another New Vegas connection. Vault 17 is one of the few vaults we know canonically got cracked open by the Master and used to create Super Mutants.
The quest to deliver the news from the Hubologist in the NCR to the leader in SF might be bugged.
While messing around in the BIS Mapper I discovered a map called BOSfield. It looks like this would be a good map to use in place of the surface map at the current BOS headquarters, to show how the location has evolved since the events of Fallout 1. Not sure if this map is used somewhere else in game.
I don't expect any of these suggestions to be in the next release, but I hope you consider them. The Megamod has been enjoyable even with the crashes and remains my preferred way to play Fallout 2. I'll post some more feedback and suggestions later.