Character Rerailment: Ben's immaturity is mostly removed to bring him back to his AF season 1 and 2 personality, with his ego manifesting in a much toned down form.
Critical Research Failure: A weird case in the fight between NRG and Lancer, where Gae Bolg fails to kill Ben. Ben explains it by NRG's armor being too thick for it, which shouldn't work, seeing how Gae Bolg always hits the heart no matter what, unless a Noble Phantasm can block it. However, NRG being an Energy Being and as such lacking a heart, his survival can still be considered acceptable, since Ben is not a magic or myth expert, and was just mistaken on the reason why it didn't kill him.
Similarly, Ben assuming Akasha and the Forge of Creation are the same thing can be blamed on Ben's lack of expertise on the subject, seeing how he is just making theories.
Of course, this being a fused universe crossover, it's the author's prerogative if he wants to make the Forge of Creation and Akasha one and the same in the story's setting. It wouldn't exactly be unreasonable for it to be done.
Also, Avenger being a Badass in a Nice Suit in civilian form does make sense if you take into account the fact the real life Joan of Arc had, according to Jean Beneditti, "a fondness for fine clothes".
Ben's Character Rerailment is even more justified when you take in account the fact that 1) He is still recovering from the event in the Ultimate Alien season 1 finale and 2) The Holy Grail is a serious situation enough for him to realize he has to stop goofing around.
Growing the Beard: The first chapter, while appreciable, was a bit clumsy, with overly long introductions, a lot of Purple Prose (Avenger's first description, especially, feels a bit like a Mary Sue portrayal) and a summoning that came a bit out of nowhere (though Word of God said he intended to explain it later). Starting with the next chapter however, the story is better written and action is better handled. It gets only better from then.
Hilarious in Hindsight: This fanfic features Joan of Arc as a Servant of the Avenger class. Years later, Fate/Grand Order had the Alter version of the character becoming playable with exactly the same class.