Not just you, I dropped a mini-rant about that on another thread less than 12 hours ago about same issue. That is a huge noob trap since newer players usually don't have a good grasp of flux level maintenance (ie, stamina conservation).
Though it is now, filling all mounts was not "a noob trap" in all releases. In releases between 0.54a and 0.7.2a, when skills were strong, speed hullmods were stronger, and some exploits were not yet removed (like vent spam and fading shots with hard flux), it was possible to fill every mount and slaughter things like a god of war. Flux management back then was not a big deal for the player who could vent spam quickly. Beginning at 0.8, when much weaker skills, more cowardly AI, and exploit removal came, filling every mount became a bad idea (although it took a while before I adapted).
What I would like to see is something like Ordnance Expertise giving bonuses for filling in mounts. Current Ordnance Expertise gives flux per OP spent on weapons. Would like to see something similar, but by filling in mounts, not necessarily by spending OP.