I also don't like their use of glowing highlights on enemy characters in the game rather than some other indicator that doesn't rob you of the graphic immersion or just being able to turn it off and figure out for yourself whom to kill. What's up with those weird sparkle effects that come on screen every now and then too?
It's explained when you play the game, and is acceptable once you understand, I guess.
I've been playing the 360 version recently; 3/9 assassinations so far, while doing every 'side-mission' on the way (except for flags, it's easier to do at the end). I have a fairly high tolerance for repetition but it's been really fun so far, and I can't say I've gotten bored of it.
The game seems to be built completely for the 360 since it IS rather pointless to do the side quests, but on the Xbox they give achievement points. Just thought I'd mention that.