There are many issues with using JGit+JSch currently:
https with authentication is not supported yet which is a very common transport used by private repos. Git (the mainline binary) uses a "credential helper" as an authentication oracle.
ssh authentication via JSch has low usability, some modern KEX methods unsupported
Esoteric .ssh/config options can break cloning because the underlying java ssh library (JSch) misreads the .ssh/config file
ed25519 identity keys supported via ssh-agent, but not via ~/.ssh/config entries. JSch gets confused when there is an agent & ssh/config
The terminal is not interactive in clojure, so you cannot accept unseen public host keys - this is probably ok, but the user might not know what to do when it fails.
Porting gitlibs to shell out to git would help all of these issues, if remains compatible with Windows support. (This is what python and Go do, shell out.) It would also alleviate many transient issues that users report that do not have associated tickets.
Proposed Patch (API Compatible with tools.gitlibs)