In EUiV I have started the tutorial several times, and everytime I get stuck moving some armies or so, because it oesn't seem to work the way the tutorial showed just seconds before.
I think both depth and verisimilitude are limited by the desire to make it possible to complete the sweep of history in a reasonable amount of time while still having the player micromanage most things.
I feel as if they've tried too hard to incorporate RTS elements, ie. you need X units at this point, or else the enemies will attack you. Now you need to research X/min, or else you'll fall behind, etc. It became too rigid.
I think they lost something from Alpha Centauri, where victory could be had with a large range of playstyles. If you held back you didn't automatically get attacked. You could overwhelm with units, small units, or go for odd strategies like adding water survivability, then nuke everyone to raise the water level. You could affect the weather, make super cities with tons of crawlers, or place a regular close grid of a ton of cities.
Apart from that the game had a lot of atmosphere, unlike for example Beyond Earth.