After some great feedback from Levi, Kamal, and the fine folks at /r/Cisco I was able to debug and (hopefully) fix the issue with Cisco connectivity. Strangely, Cisco’s implementation of the SSH protocol refuses to acknowledge, and in fact disconnects, any client attempting to change the “window size” of the connection during shell negotiation. The window size determines how much data can be sent over the connection before having to re-adjust the window size. I’m no expert, so I can’t explain the significance of this, but it appears the fix will be simple. Alternatively, if the fix causes compatibility issues with other SSH servers, I will be able to at least enable an option for delaying any window adjustments until after shell negotiation, specifically for Cisco routers. So far, the fix appears to not affect any of my test environments. So, Release 8 will contain a fix that allows connections over SSH2 to Cisco routers. This requires an IOS version of at least 12.1, from my understanding. Eventually I would like to add SSH1 and even telnet connections to the possible connection types; however, there are bigger usability fish to fry at the moment.
Once again, I sincerely thank everyone for their feedback and support. Without it, SSH Terminal Emulator would not have made it this far.