Have EMP 'nades burn % base battery charge based on their tier? 80% for tier 1, 90% for tier 2 and 100 % for tier 3? So for example if your battery charge is at 80 % an EMP 'nade will still burn it all, but if you have full charge it will leave you with 20%.
Suggestion is mostly based on enemies who use EMP 'nades during naval combat. Burning away all the jet charge is difficult to bounce from - the Protectorate Marine patrol is unreasonably strong in this regard. In the mean time it will give the player bigger incentive to craft higher tiers of EMP 'nades.