This is one of the reasons why softlists exist, just audit the games you have for each system and move them to their own folder named after the system's parent set, and put said folder inside "roms".
Then whenever you want to load a game you just have to select the "Software list" option under the File Manager and choose from the list which will appear, no folder navigating necessary.
For games not in the softlists, I believe that MAME saves the last used directory (used to hang if it didn't exist anymore), so you'll only have to browse through the folders once per system.
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