I think the most practical way to expand the GameShell’s I/O would be to create a new module that could link to the ClockworkPi, not alter the construction of the base board. The module could contain 2 USB A ports (one of which could be a powered host, though I’m unsure how viable that is for the battery) and an HDMI output.
This module could be used in place of the LCD screen, though I’m not sure how these could be linked up to the ClockworkPi board itself (any ideas for this?) This would, effectively, turn the GameShell into a retro console like an NES Classic or a Raspberry Pi running RetroPi.