It would make a big difference, because instead of following markers on a map, you would investigate.
And it's not just eagle vision. It's audio (if you hear a town crier) and alot of simply walking around in the general area you were directed, peaking around corners, running along rooftops etc...
Also, it would really force you too work in order to get the best Intel. The best intel is also the hardest to find.
For example, the best missions are pickpocket, as that usually gives you a map, which you can view in your inventory, but this is the hardest to locate because the people are usually hidden away.
The easiest ones to find, and also the least useful, are the interrogation missions usually a town crier, you can find him and beat him up fairly easily, but you're not going to get a whole lot of useful information.
So basically, alot of the work would be investigation, and it would decrease teh repetition since it would be much less likely for you to find all 6 clues, instead you would probably find 2 or 3 per missions and move on.
It really does seem like the game was intended to be played that way. So many of the design decisions are completely pointless when you can simply follow a marker on a map...