If you don't need immediate access to the packet payload, I've been enjoying Brim Desktop [1]. It comes pre-packaged with Zeek (formerly Bro) and gives you a UI to view and query those Zeek logs, which will link flows together. It also supports opening specific flows in Wireshark for deeper analysis. It might not do everything you need, but it's improved my pcap analysis workflow. It's free at the moment, and this part of the demo [2] gives you an overview of processing a pcap.

[1] https://www.brimsecurity.com [2] https://youtu.be/InT-7WZ5Y2Y?t=382

I wouldn't be surprised if JaneStreet open sources an internal tool soon-ish. They've actually been writing a number of custom plugins and modules for WireShark to support internal custom protocols and seem to have a lot of features they'd like that aren't currently present in WireShark.

Surprised nobody has mentioned it yet, but some of the best network engineers I know will use a combination of `tcptrace` and `xplot`. It's on the command line of course, but graphs can still be generated and I think it's more performant over a GUI (for large pcaps).

Web-based, but may do what you want: https://arkime.com