@kal318 Yeah, I think you are exaggerating problems with hotkeys. Retropie does not have a problem with hotkeys. This forum is filled with people who have questions, and questions about hotkeys come up often, but the issues come from a misunderstanding of retroarch/libretro framework combined with the fact that none of us use the same hardware. I use a keyboard controller (IPAC) with arcade controls while you might use a particular gamepad, and we both made different choices at first-run about what buttons we map to what functions, or what changes we made in our .cfg files. It is a source of confusion, and a configuration choice that needs to match the need, but I would not call it a problem.
Case in point, you say keyboard hotkeys are working for you. It probably means you have a keyboard key assigned as the hotkey which would be perfectly normal for me since I use a keyboard controller. It is not a problem, just a a different configuration. It would be like me saying there is a problem with sandwiches because of all of that disgusting mayonnaise I always find. Add me to the list of dry sandwich lovers who cannot find a solution to this mayonnaise problem.
In any case, Your question is a good one and we can probably get you straightened out, but you need to add a lot more detail about your configuration as @mitu suggests above. For example, how did you build your system? We have seen a lot of time wasted on misconfigured third party images where we have no clue how someone else might have messed up choices for you.