My thinking is more along the lines with Bear. I think that the quick loading missiles upgrade is rubbish. It's only useful to new EA players that don't know how to properly use missiles. As as personal view breakdown I see it this way...
Pros...
You don't have to worry about timing your shots since you suffer less penalty.
Cons...
You take longer to deal damage; since you deal full weapon damage every even turn instead of every odd. So instead of dealing full damage turn one and then again on turn 3, you have to wait until turn 2 and 4.
It's harder to bust through interceptors.
End result...
This just makes them slower to deal damage and easier to use. Thus this simply takes away the tactics required to use them and makes them easy use newb friendly weapons with no flavor. It also means that, since it takes them longer to dish out their payload, that you risk losing the bulk of your fire power since any missile ship destroyed on turn one, three or five, has not yet had the chance to dish out its full potential due to its immediate payload being cut in half.
Essentially this means I never, ever, ever get refits on ships with missiles. The missile blitz, as I like to call it, is one of the EA's strongest weapons. Sure we have ships reloading on turn 2 and 4, but on turn 1 we show our enemies just what it means to screw with EA missile boats. I find that the slow-loading gives the missiles flavor and forces you to use them tactically, since a poor choice in firing them actually carries consequences; the Apollo is of course immune to this statement due to its total kick butt special rule.
One of my favorite tactics is planting some missile boats in a position that forces an opponent to either hide or face the full brunt of a missile barrage. This tactic is ruined by quick loading because my opponent knows that any damage he takes with be cut in half and will thus make it much easier for him to survive a round a shooting. Which also brings to thought the fact that one of the advantages of missiles is their long range. This is an advantage that is greatly reduced by granting ships that could've been killed in one round of firing a chance to close the distance between them and their missile firing target so that they can return fire.
I don't care what anyone says. This refit is a downgrade that is completely useless to anyone planning on using missiles in a tactical manner. Makes them slower to deal damage and more vulnerable to lighter, faster moving ships. This upgrade is almost as bad as the Narn upgrade that lets you send a ship away for 2 turns just to change its model. Whoever was in charge of the EA and Narn upgrades needs their head examined.