The sad thing about it all is both games had a pretty bad start. But everyone is going to praise Civ V for being amazing while continuing to trash this game. When they both suffer from the same exact problems.
CAVEAT: I've only put about an hour of "fiddling around" time into Civ 5, so I have yet to see some of the more potentially braindead combat AI and diplomacy issues, so I'll address neither in comparison to Elemental (which is godawful in both respects) except as meta issues.
My own personal experiences are quite a bit different for each game, and from what little I've seen Civ5 is lightyears ahead of Elemental in many ways.
Crashes and Instability - Until Elemental 1.07, I ALWAYS got a crash to desktop when alt-tabbing with Elemental. Since then I've gotten fairly consistent out of memory errors doing so (and during fairly long games). In addition, late stage games start to slow down pretty painfully on my still pretty snappy system (i7 920, 6g, GTX 275 with the most recent drivers). I've seen nothing close to this for Civ, though I need to push towards a longer running game to see if it holds out. I do enjoy your snarky comment about the "blue line they drew in microsoft paint" in reference to a river in Civ. Civ's graphic are so far beyond Elemental that I guess you'd refer to the latter's attempt at inland water to be "bad ASCII art" or the like
UI - Civ's works. It'd definitely way too spoonfed compared to Civ4 (for my TBS dollar) and a bit too much in your face, but it's in complete opposition to Elemental's bland, confusing and in some places missing "UI".
Combat - To be honest, I was never happy with Civ's way too abstracted view of combat in general and it seems to have taken a distinct turn for the worse with the hardcore overpowering of artillery or the AI being too interesting in just rushing you one at a time akin to those cheesy martial arts flicks from the 70s and 80s. That said, it's still Einstein compared to Elemental's Special Ed. Short of abusing mechanics (such as the outdated 10 damage to all enemy targets minion spam), the AI is pathetically easy to beat in any combat situation unless I somehow forgot to bring a single caster. Or hell, even a horribly overpowered melee sovereign (pre 1.08 perhaps, still not sure on that).
Game Mechanics - The base framework for Civ (building, research, culture, etc.) are still working pretty damned well. Show me any one part of Elemental that works on it's own (magic, combat, building, diplomacy, AI, unit design, dynasties, questing, resources) let alone as part of a greater whole.
To sum it up, people who want to compare Civilization V's issues with Elemental's need to do 1 of 2 things.
Either admit that you're hopelessly in love with Elemental and can't get past the rose colored goggles. If this is the case, embrace it and just wait for Stardock to just make a great thing better (as has been posted by any number of people).
Or realize that while Civ has it's flaws, it's fixable with tweaks and a powerful modding community. Elemental still needs the basic FRAMEWORK to be fixed before modders can do anything but patch the biggest holes. Elemental *MIGHT* someday be a great legacy game like MoM (or to a lesser extent AoW) and we'll look back on this time as the dark ages before the great enlightenment. And while I'm regaining more and more hope that it's coming (given a number of pretty heartening and posts about specific issues by devs and Frogboy), it's still going to be a long road to recovery.