"Some ROMs are marked as 'Not Working' but I know they work in newer MAME" Solution: That’s correct. 0.145 lacked drivers for later revisions of certain PCBs. If you need a game like Pokken Tournament (a 2015 arcade game), you’ll need a modern MAME version anyway.

"My joystick doesn't work in-game" Solution: MAME 0.145’s input system is per-game. Press Tab during gameplay, go to "Input (this game)", and map your controls. Use ctrlr files for global mapping.