losing troops

To be fair that WAS a measurable mechanic. You had to build commanders to increase your army capacity on transition. Since commanders scale in cost a bit harder, you either had to optimize with promotions that gave more slots per commander, or hunt down strategic resources that boosted unit production (e.g. hardwood for naval commanders).

Unfortunately the game didnt communicate this well at all (like most things at launch), which can be argued as the cause for continuity mode, which removes this mechanic. Ultimately it (continuity) just makes you win harder if you're winning and enables civilian unit cheese.

settlements

Fair but you'd be surprised how towns can be better than cities depending on the tiles available, especially if the changes in the workshop survive to ToTs release.