I would like to get some opinions on the best design when connecting Layer 3 switches (in our case, 6500's) across an ethernet type WAN (basically, point to point fiber).
The way I see it, there are two options. You could configure the interfaces as 'switchports' and then only allow a single VLAN across the port -- although still leave it configured as a trunk and have a native vlan which is not configured on the switch. The problem I see with this design, is that there could still be problems with spanning-tree as you could exchange BPDU's across the link. Unless you block them. Here is an example:
switchport trunk encapsulation dot1q
switchport trunk native vlan 4094
switchport trunk allowed vlan 86
switchport mode trunk
no ip address
ip address 18.104.22.168 255.255.255.252
The other option is to not run the interface as a switchport, and leave it configured as a layer3 interface. In this case, there shouldn't be any problems with spanning-tree. You do lose the flexibility of running another vlan across the interface if for some reason in the future you had to do so (for example, in a disaster situation).
So, with all that being said, what is the best practice in these types of situations?