the waypoints are HORRIBLE for bots, like some arent even connected

something that i noticed is that the supercapacitor for the mech doesnt recharge

If you mean the junction compartment, then yeah that's my bad. It was walled off in it's own hull as a primitive form of water protection so that if the airlock was opened when not docked it wouldn't damage the junction boxes.
I've pushed an update adding a door so that it can be drained if necessary. Thanks for letting me know.

I mean, if you look at the mech cockpit, there is a piece that isn't connected. The piece under the navigation monitor. It has a gap between the hulls that I was able to fix so it could drain

Well actually, the mech has a hull piece that isn't attached so it can't be drained.

Do you have it powered on? The mech uses two relays to toggle between charging off the main sub and distributing power to the main systems. These two relays are controlled by the button on the shuttle battery, which starts in the off position in order to ensure the shuttle charges on mission start.

Based upon my testing the mech can and does drain water so long as the shuttle is off recharge mode, as the power inside the battery will not flow to the junction boxes while the battery is charging. This is indicated by the lamp above the control console. If you can see the red light component, then the shuttle is currently charging. If the lamp is white, power is being distributed through the junction box and the shuttle is operational.

Be aware that the shuttle itself does not use a standard automatic docking port and thus the hatch is only manually controlled by the internal and external buttons.

Mech fills with water and can't drain!

Fantastic work if this is your first sub