I actually preffered the lack of stacking in Civ V. Felt a bit more like other tactical games (like my beloved Hearts of Iron 3), where putting too many units in one place = doomed to failure. The doomstacks just got rediculous - kinda worked for the early game, where that's kinda how armies generally operated (one bigassed blob that runs at a specific target), but y'know, it just felt gamey and cheap. Without logistics, ability to attack multiple units in the same square, you could practically have an immortal army blob running around the map without a care in the world. At least, now that unit stacking is gone you actually have to be careful in your strategy, pay attention to territory and positioning; if they manage to wipe out one of the older units you have holding a flank, they get free reign to wipe out all your precious artillery and support units who aren't meant to be fighting one-on-one, so you have to make sure to hold a line around the units who need protection, rather than just chucking them into the super-blob and feeling safe that there's 20 billion riflemen units there to protect them no matter what happens. It's kinda neat, and reflects the macro-level territorial control that constitutes so many wars in later history.
Also there's no feeling like punching through a line and wiping out 6 tiles of archers. That just makes aaaall the deaths worthwhile :p
Also the resourcing system is a bit more developed. I always found it annoying in the older civs how an entire empire could live off one deposit of iron, and fire out a billion tanks, aircraft and ships because one city a continent away had a single iron mine.