Flux Capacitors in the CEF are currently much more powerful than GT batteries, with basic flux capacitors holding 20x more than basic LV batteries. They are also easier to craft and can charge items in the inventory. GT batteries do catch up around IV but at that point power is mainly stored outside CEFs anyway.

Either the power levels of flux capacitors and GT batteries should be balanced, or quests relating to the GT batteries should be removed such that new players don't use them in favour of flux capacitors.

The capacity of Flux Capacitors was intentionally buffed by Damien, and when he polled whether the community wanted to be able to keep using them in CEFs or only permit use of GT batteries, the response was overwhelmingly in favor of keeping things as they were.

GT battery quests remain useful because you will need to make all of the different GT batteries eventually, even if only for creative items. Alternately, someone might want to use a device like a Battery Buffer which does not do power system conversions so you need GT batteries.