I can only guess that the intention is to show that this isn't Freespace. Not having played Freespace, I don't know how this in-flight re-arming would have worked, but the only time in Wing Commander that we get in-flight re-arming (from what I recall) is from the shuttles in Prophecy. I'm pretty sure the tankers in WC2 only refuels the Broadsword, not re-arms.
Yeah, in WC2 you only got fuel, not missles. The Freespace inflight flight rearm was basically a shuttle that would dock with you when you called it to. It would resupply you with missles and countermeasures. It wouldn't refuel you cause your afterburner would recharge on its own. I'm not sure how many times it would be available after the first rearm, but in the training mission it says the supply is limited. It was nice, and since the capability was with the original game and we see something similar in both WC2 and WCP I was curious why it wasn't in Saga.
As for the Excalibur, having gotten to those later missions, I can assure you that it doesn't feel like I'm just sitting back smiting the cats with Zeus's thunderbolt anymore. I have had more than one "thank god I'm in an Excal, not something else" moment in the past few missions.
Edit: Just saw your comment Aginor, thanks for the reasoning.