Lack of distictive Civ design. The sheer number of civs required for the number of ages they had resulted in designs that weren't particularly memorable to me, and primarily just seemed as generic bonuses (do I want the culture bonus or the prod bonus). I worry about this for Civ 7 as well, but tbd.
One thing I am pretty confident about with FXS is that they have a very good track record regarding bonus designs and numerical balances. Amplitude has already suffered from too heavy snowballing in the late game since the EL years, and HMK amplified this issue by stacking more bonuses every time you change a culture - and you change that five times in one game. This means the cultures need to have very generic bonuses, and even with generic bonuses, the numbers get out of hand very easily.
A small example. In Civ 6, the earliest offensive unit is the Warrior, which costs 40 production. The late-game offensive unit is the Tank (excluding GDR), which costs 480 production. This is a 12-time increase. Civ 5 has similar numbers.
In HMK, the earliest offensive unit is the Archer, which cost 90 industry. The late-game offensive unit is the Main Battle Tank, which costs......14805 industry. That is a 165-times increase. The game basically expects a 165-fold increase in your production capacity.
Indeed, in late-game HMK, it is very common to have a city with 10k production to build districts that cost 25-30k while only providing about 200 yields. Stacking generic bonuses constantly = numbers get out of hand in the late game = not many meaningful choices in the late game.
Meanwhile, with FXS's track record, the age transition "soft-restart" mechanics, and the number we saw, the balance of Civ 7 won't be this off, and the numerical choices should be more interesting.