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That's good to hear about the custom firmware, looking forwards to trying it.The custom firmware is currently in testing, it should not be too far away. Regarding the ROMs not being in alphabetical order, on the custom firmware you will have them in alphabetical order. They already display in alphabetical order, but for some reason the manufacturers put numbers before the names (maybe their favourites) so they go in that numerical order, adding your own will be alphabetical. Custom firmware will have many more systems emulated and improved performance.
TV output is via RCA so it will always be lower quality than HD, more SD quality.
I did not have any issues with the arcade joystick, but I do have a self built arcade at home so I spend a lot of time on it. Arcade sticks take a little getting used to compared to a D-Pad for example.