Well ... I just got it and it isn't as good as Master of Magic but at least stacks of units that end their turns on the same tile don't get their orders cancelled like with AoW:SM. (I think one unit could actually get "hijacked" by another's move orders if they happened to end the turn in just the wrong way, but I haven't touched AoW:SM in years.)
WoM has serious problems, don't get me wrong, just nothing quite that catastrophic. The main annoyance is that all units in cities are treated as if they were on permanent garrison. This is a problem dating back to GalCiv 1 that's never really been addressed.
In GalCiv 2 using planets for repairs was really super-duper important, but the only way to keep track of which ships were orbiting which planets was to either take notes or memorize where you put them. Any ship in orbit around any planet was treated as though it were a part of the permanent garrison.
Master of Magic had a "guard" order and an "active" status, and that status didn't change just because you put a unit in a city. You had to explicitly give the "guard" order, and once you did the unit stopped asking for move orders. That is a superior game mechanic; you can't assume that any unit that goes to a particular place will never want to leave. You can assume if the player says, "Stop bothering me," that that unit is where it needs to be, whether or not it's in a city.
By the time of WoM the Stardock people had figured out that something was wrong with their system -- you get alerts any time an injured unit is fully healed inside a city. Too many GalCiv 2 battleships in need of repairs ended up disappearing into Raiders of the Lost Ark packing crates I suspect. Those "unit healed" alerts are made necessary by a game mechanic that doesn't distinguish where a unit is from what the player expects it to do. Location-dependent unit behavior is I think the core flawed assumption that makes "fixes" like the "unit healed alert" necessary.
Once you start using your cities in WoM as railroads the annoyance factor turns up to 11 (or over 9,000 depending on your taste in pop culture). You will be constantly moving units through cities, and the AI isn't good enough at the pathing to do it for you, which means you'll be sending a constant stream of units into your cities then popping them back out again. This is a huge pain in the rear. If "Auto End-Turn" is enabled you have to leave some other unit active to hold your turn open, so you'll be constantly switching back to the unit you actually want to move. I can't imagine having "Auto End-Turn" enabled, myself; I do all other moves first then save the "railroad moves" for last so I can follow the unit I'm actually trying to move without being interrupted.
But wait! Without "Auto End-Turn" enabled you have no way of detecting idle caravans. *sigh*
So yeah lots of petty annoyances, but I'm enjoying the game despite the occasional hair-pulling episode. It could've been a lot better, but it's not too bad even with the punishing user interface factored in. The Goodie Huts are also cranked up to 11, which keeps your heroes running all over the map and promotes getting you out there exploring.
The food scarcity situation is also a really interesting twist. Your cities are only as good as the resources supporting them. We've done the "spam a hundred cities" thing in a hundred games that came before. Making cities cheap to build but expensive to support really changes things up. But then that too is brought forward from GalCiv, isn't it? "Not every 'habitable' planet is a place you'd actually want to live," was the warning about Class 7 planets I remember well -- after actually settling one and discovering firsthand how bad an idea that was.
With the "fantasy version of Fallout" back-story WoM can make food scarce and bring back the settlement limitations we fondly recall from GalCiv. That part works really well, at least for me. That's probably my favorite aspect of the game. In my first game one of my cities was burned to the ground and suddenly all my other cities, stuck at level 2 and sucking up my gold, could become thriving level 3 and 4 metropolises earning massive profits. "Oh, that city they burned was actually hurting my economy, wasn't it?" Epic.