Liked in MTW

Importance of battles - less of them, and generally more meaningful than RTW battles.
Dismounting (some) mounted units - Chivalric knights became an impressive anti-armor, anti-cav death squad when dismounted. Perfect when you have lots of knights facing spearmen - have them dismount, and a weakness becomes a strength.
Capture/Ransom - capturing instead of killing routers makes more sense (and was handled better than in RTW). Plus, ransoming back prisoners, especially members of the Royal Family is a great way to make quick money. More than one king has been forced to make me rich to be ransomed back.
Multiple Time periods - you don't have to start at 1080 every time. There was also a start time at 1231(?) and 1321(?), giving you different technologies, factions, and amount of time to finish a campaign.
Rally units individually - Instead of pinning your hopes on a general, the assumed commanders of single units could rally that unit. Very useful, and you can still rally and make a stand if you general dies.
Funky naval movement - Setting up ship lines connecting oceans was a little weird, but I think it works better than the broken naval work in RTW.
Agent movement - moving agents between any province with a port really worked, connecting empires and letting diplomacy and agent interaction happen without the micromanagement involved in shipping agents overseas and back like in RTW.

I like some things in RTW, like city population, being charged to queue units and buildings up front (I hated the "Insufficient Vespene Gas" messages ). There are more things I dislike in RTW, but I won't bring them up (other than what I've mentioned so far.)