Audio Interface Connections - best one today ?

there is no right answer it depends on the interface manufacturer
while PCIe would be the lowest latency the difference from a PCIe and a GOOD Firewire/USB is only .75ms
PCIe tends to be expensive and require converters.

RME regardless of connection is the best.
Motu, Steingberg,Lynx (with USB card) are not far behind.