StingingVelvet: That's what it has become, IMO. Sending assassins across the world, tower defense, naval combat, crafting and hunting... it's all mini-games, or at least things well outside the realm of stabbing dudes and exploring ancient Jerusalem, which is why I loved the original.
I agree that tower defense style missions and naval combat missions are annoying distractions in games that aren't tower defense games or naval combat games,
if they are mandatory for the story to progress. That's why I don't think Saint's Row 2 is a good game - it forces you to do several mini-missions to earn "points" so you can unlock progress in the main story. However, as optional side missions they can sometimes be a nice change of pace, and you can choose which ones you want and don't want to do.
However, it wasn't naval combat and tower defense I missed in AC1. It was more varied mission locations. For example, let me sneak into a ship to kill the captain, and on the way there, have me steal a key from someone or blow up a lock or something. You know, just make the missions more...
missiony.
Oblivion actually had a few pretty cool assassination missions. In one of them I had to kill a dude and make it look like an accident (, so no stabbing, that never looks like an accident), and in another I had to sneak into a house and kill the people in there without any of them seeing me killing any of the others.