I feel like Egypt just has 1 objectively badly designed element (the necropolis) and 2 undertuned ones - navigable rivers & Tjaty.
All of the unique “great people” are a bit clunky. There are 10 of them for every civ that gets them, they’re all unique, they have escalating costs… it’s a cool idea, but it’s messy. This is for all of them - Tjaty, Shi Dafu, Ulim, etc. Many of the individual units have good abilities, but this is just a nightmarishly complex little Rube Goldberg machine to give out little boosts. I’m not sure what to do with them generally.
The necropolis is just inherently flawed. There are so many interesting effects you could give it - say, it grants yields to all wonders in the city. Or maybe it gets yields for every wonder within X tiles (like cov6’s temple of Artemis and camps.) 100 gold for each wonder built is mathematically terrible and anyone could have foreseen that without playing the game. Suppose you have a real banger of an ancient age and knock out 7 wonders. That’s potentially 700 gold if you even built the necropolis first in each city - probably more like 500. That’s just a few gold per turn at the empire level. Does no one remember the burial tomb from civ5? Now that slaps.
I think the problem with boosting navigable rivers is it misses the obvious- the land
adjacent to navigable rivers. If we could boost that instead, well, yeah, then you’d change your tune about Egypt. If I got +1

on improvements
next to a river, oh, we’d be cooking with gas. Slap on +25%

towards quarters next to navigable rivers and Kemet just
sails, baby.
Egypt was known for the stuff they built on the Nile’s banks, not what they did in the river itself.