There is a difference the way both the connection works. Although they will have the same purpose but there is the difference the way the switch ports will work.

 

In case of a SVI you will have eventually a Layer-2 link between the switches. This will run your normal STP and other control traffic between the switches.This will extend your STP domain from a switch to the other switch.The ports will go thorugh the normal STP states and in case of a link flap or link going dowm/coming back the recovery time will be a little high.

 

In case of a routed port between the switches,you will have a layer 3 link between the switches and will work as a normal router port. There will no STP running on the ports and the STP domain will not be extended beyond the downstream switches.Applring layer3 features like ACL's,PBR's will be a ltille easy in this case.

 

The Disadvantage of running routed ports is that each port will be a separate network and you will have to manage a large number of IP subnets on the network. Running a routing protocol will be a good idea in this case.

 

My suggestion for running a point-point link between 2 layer3 device would always be a layer-3 link. But this also depends on the kind of network topology you have.