> So could the batteries not be isolated from each other some how? With diodes or something.
That would be safer, with a diode in each half of the charging Y lead. However you can't prevent one battery hogging all the current so the charger must only be powerful enough for one battery, and overall the charging will take twice as long as with a charger for each battery.
> Suppose you come home late at night and set one battery to charge and go to sleep the next day you wake up to only one charged battery instead of two.
Large batteries like yours would usually come with a slow charger and in one night it may not charge both much beyond half way. A charger's designed to cut off when fully charged by detecting low current, two batteries will take twice the current and it will take longer to cut off if at all, which can be dangerous. Oh and it's widely advised not to charge while sleeping except outdoors.
> Or perhaps have both batteries connected but only charge one battery at a time.
> So when battery 1 is fully charged it would switch to battery 2.
> Or have a timer that switches battery each 30 minutes or so they get charged about the same rate.
This is uncommon with bikes, you'd have to DIY it which (with postage) may come to nearly the cost of a mass produced charger... which is one reason it's uncommon. Your idea ought to be OK but, unlike cars and USB, ebike batteries aren't properly protected to the extent of fully controlling their own charging. The result is a mess for the consumer, needlessly cumbersome, restrictive and exasperating and it compromises safety, but it does facilitate lock-in for proprietary vendors.