And yes, having 10 or more primable items on board is quite unwieldly.
There was some thought of limiting the amount of primable equipment on a per-ship basis, analogous to the way missile slots work, including a 'sell all primable equipment' option when in the F3 screen. It's an option we might revisit...

Anyway, one thing that is very likely to happen in trunk is the addition of a new HUD 'dial' to specifically display the primed equipment name, rather than relying on the player remembering which equipment was primed while in the middle of a fight.
Finally, each piece of equipment is a customisation to your ship, and I believe the order you bought your custom equipment influences the order your equimpent is shown to you. Each ship gets extra individuality this way, which is - in my opinion - a fairly good thing.
Mind you, if what you're saying is that the order of primable equipment changes randomly from savegame to savegame then that would be a bug, and we'll try and investigate what's going on there.