I have no problem with 1UPT system - it worked great for PG and I can see it working great for the Civ series as well.
The only thing I'm slightly concerned about is the scale of the maps - PG worked because in general there was plenty of terrain in and around objectives to maximize maneuver. If it's true that infantry are being given the 2 hex movement range they need to make 1UPT work, (and presumably tanks and cav 4-5 hexes) I hope that means maps are increasing 1.5-2 times current dimensions for a given number of cities to give proper room to maneuver. (ie trading space for time, penetrating front lines to attack artillery from behind, cutting off wounded units path to escape, etc.)
Obviously they didn't agree with me and made empires MUCH smaller.
The result is a given number of units is compressed into a much smaller amount of terrain with less room to maneuver and ultimately results in the the type of failings you list.
Cramming 20 units forward on a less than 10 hex front against 1 city at a time in sequential fashion with subsequent cities being only 3 hexes away has killed the operational depth of the game and resulted in the tediousness of having to "shuffle" units around which places a premium on the AI. Because roads are so short there is little point in trying to use them for movement as the "end" will quickly become cluttered.
On the otherhand those same 20 units advancing on a 40 hex front with a choice of 4 or 5 border cities to strike at and 7-10 hexes depth beyond till the next "row" of cities would have made for much more interesting and varied operational options - fighting withdrawal, elastic defense, flank attack, feint attacks, multipronged offensives, etc are all things that would have been experienced to advantaged with greater depth.
3) It distorts the rest of the game. Civ was designed around a different paradigm, and the changes needed to avoid unit overpopulation made the peaceful game imbalanced and boring (e.g. weak production and high costs for large empires, both driven largely by the need to avoid massive unit production.)
I don't think this was a specific consequence of 1UPT but rather the design decisions to "streamline" the game in order to appeal to people who didn't want to build 20+ city empires, or build every building in every city.
4) It's prone to artificial tactics...
Yes but let's be fair and clarify this has nothing to do with 1UPT. Stacking could be equally victim to a poorly designed IGOUGO combat system.
5) The new problems created with 1 unit are worse than the big stack problem they solved.
Again I think an argument could be made that 1unit was fine but the problems were created by not designing the size of the rest of the game in a fashion to accomodate it.
Solutions? A modest stacking limit, either with overstacking allowed (but only the "limit" worth of forces permitted to engage in military action) or the AI coded to keep itself 1 or more below the limit at all times (to allow movement.)
The problem is stacking still feels artificial unless you come up with a good way to manage the combat between stacks - in Civ4 for example suppose you had 2 identical stacks with an axeman, a chariot, and a pikeman each. The "loser" is automatically the one who initiates the attack - regardless of terrain, location, etc - because the attacker
always has to face the defender best suited to beat him. While to some extant that was a deliberate counter to the disadvantages of the IGO UGO turn structure, it also means that the only viable tactic it to defeat an opponent is mass superior numbers against him.