E2 vs. E2Lite on RA series

Until now I have been using E2 Lite for multiple product developments on RA6 series with FreeRTOS and FSP. I have had several occurrences where single stepping code becomes difficult due to interrupts and context switches. I had hoped that single-stepping would follow only the current thread. I have also noticed that single-stepping a longer section of code sometimes results in the debugger disconnecting from the target.

Note: I have flash breakpoints disabled.

I'm hoping someone out there has relevant experience and can help me with some advice.

Am I expecting too much from the E2 Lite? Is JTAG better and/or more reliable than SWD? Does the E2 provide a significantly better debugging experience than E2 Lite?

Thanks in advance for any info you can provide.