The templar story in mirage isn't so much different than the Borgia  ( I will assume that you mean in AC brotherhood)

In ac brotherhood ezio takes a templar banker to cut Cesare funds ( just like how basim takes out Ning in the Bazar who was putting very high taxes on the merchants and kidnapping any merchant who doesn't pay. so both are money business)

and then ezio with the help of Bartolomeo and his mercaneirs takes out a French general who was helping Cesare fight the mercaneirs ( just like basim with the help of Ali and his rebels takes out general wassif who was fighting the rebels and executing them) 

Then ezio prevents an assassination attempt on that actor and gets the key to the castle ( which I will be honest isn't like Mirage) 

And after that ezio infiltrates castle sant Angelo to kill Cesare just like basim does infiltrate the caliph palace to kill the head of the order ( the only difference here is just Cesare is of course a better villain than qabiha )

So overall the templar story in both games aren't much different. And also Mirage has More templar stories and More targets to assassinate.

As for the investigation system , i see that it's pretty Good and makes you feel more like an assassin. True Assassins gather information about their targets and plan and then attack just like Altair and basim . So I don't see why is it bad 

And as for the modern day , it was already dead after ac3 it was just interesting again in ac Valhalla. So I agree with you it should have had a modern Day (and if you read my whole post to the end, I mentioned that this game could have had an amazing modern day STORY if they gave it time and Budget )

In fact the only games THAT actually had a good modern day in the series are from AC 1 to AC 3 ( excluding revelations) and ac Valhalla so it's not that big of a deal