The LimeSDR id best suited for USB 3.0 operation - it’s not advised to use USB 2.0 when running the LimeSDR with other applications. Certainly PCIe would be faster since you’re at the edge of the PC’s hardware and not dependent on an I/O with an abstraction layer (like USB) to add latency.
Latency will always be an issue with Software Defined Radios of any kind and the interface they’re connected to. No matter which SDR you end up with, each will have their own ‘bottlenecks’ that are inherent to their own design and to the interface they use to stream their data. I’ve used the LimeSDR on a number of different platforms (PC, LattePanda, UDOO card, Pine64, etc) and with Windows and Ubuntu OSs. One thing is clear - you have to have a computer that runs at least at 2.2GHz and has USB 3.0 resources for the LimeSDR to be effective. As I mentioned, it’s not recommended that you run the Lime on USB 2.0 - it’s performance will be severely limited with the app it’s coupled to.
Hope this information helps - 73 de Marty, KN0CK