I agree. I plan to try out the Legions mod to see if that helps and see how my game experience goes and whether it's more enjoyable, but from doing some reading, I have a hunch that once you get rid of 1UPT, you still have a broken system. 1UPT seems to be a core element of Civ 5's design and simply "modding it away" by allowing you to stick more than one unit on a single tile won't change some of the economic issues that are apparently pretty closely connected with 1UPT.
PI-R8 had an interesting post that I read on another site which went into a LOT of detail about how the game systems function, which I won't repeat here. Google "PI-R8" and "1UPT" and see if you can find it. In short, much of the game seems to have been designed to accommodate 1UPT, especially with respect to the speed at which your civ develops.
I'm not sure if this is the truth, but I would believe it if it turned out that the underlying design was to make the game super-duper pretty and focus heavily on graphics. This, in turn, eats up processing power as it can take a LOT of resources to animate all those tile animations, render FOW, and move units around, especially at high resolutions which will show off such gorgeous graphics.
This, in turn, means you need to cut down on what ELSE is going on in the game. Things like, say, calculations. The more stuff you build in your cities, the more the game has to check benefits, bonuses, maintenance, etc. And all that is CPU time that ISN'T going towards rendering pretty pictures. Same goes for...waaaaaaiiit for iiiiiiiit.....
Units.
Imagine having 50+ unit stacks running around the map. That's a LOT of calculations to handle, especially if the AI is tasked to operate that way too.
So, what do you do? Everything in your power to prevent large armies from being built. You limit the space that they can occupy via 1UPT, so that you can render smaller maps and show off the pretty. You limit how fast they can be built by increasing build times. You limit how fast other improvements (buildings and tile improvements) can be constructed, so as to slow down how fast a city gets more bonuses that help it build stuff. You slow down city growth so that, even with a dynamite site, by the end of the game, you may only have 20 pop in a given city. Nice, but not as big as older games could get.
I dunno. I haven't gotten as in-depth with the game to find all this stuff out first hand, but I can see how what I've seen of the game could end up working out that way towards the end game. So, yeah, ditching 1UPT might make combat different (better? Depends on who you ask, I guess...), but it'd still leave a LOT of work to be done. So, I guess it's not as simple as adding an option of "1UPT or stacks?" in the Advanced Setup. I'll still try out the Legions mod to see how it goes, though. After that, I suspect I'll be retiring Civ 5, though.