Optimal use of skimmer is more than that: Why waste charges when there is no immediate threat or short miss-able opportunity (like punishing a phase cloak cooldown)? Use it when you need to actually dodge a big hit/burst. This way skimmer helps to win flux war, rather than just increasing mobility a bit.
Or to get behind a vulnerable ship, when you aren't fast enough to do so otherwise (or it would cost too much shield flux).
Skimmer system is not particularly strong overall (for a Medusa anyway), exactly because it recharges so slowly.
AI uses all mobility systems in same stupid way: "I'm going somewhere, can the system get me there faster? If yes, use it." There is no attempt to conserve system use for best opportunity or move ship in way that makes system more useful (turn a Plasma Burn ship ahead of engagement, and engage with broadside, etc). At best there may be some suicide checks on stuff like Burn Drive.