Units are individually upgraded which breaks the RPS system, and creates all kinds of imbalance between the units and weird unit combos.
I agree completely . We removed the ability to upgrade units from Napoleonic 2: Total War and I can say it's working very well; I can't recall a single complaint about it! Not only does it improve game play (although that can debateable) it also reduces setup time as buying armies is much more intuitively.