I don't think that the loss of utility slots hurts BS a lot for missions.
It is way faster if you change ships after a few missions and salvage with a noctis.
Not everyone lives at the end of a tunnel or does missions for only a single corporation. Personally, if I do three or four missions in a row it's entirely possible that no two will be in the same system. What about epic arcs? What about people who maintain positive standing with multiple factions and therefore have multiple mission hubs? It's slow enough moving a mission ship cross 10-20 jumps. Having to make a second trip in a shuttle then return in a noctis...and then again to get home...is ridiculous.
Utility slots are not a game balance issue. They are a gameplay convenience issue.
Even if you are running for a single corp, missions usually lead you to 2 or three different systems. I don't really see a problem there. 10-20 jumps is nothing, but maybe I am just used to jumping around a lot (in a BS, yes). You usually don't switch systems very often. If you run for even only a few hours, I think the noctis would be worth it. Or, if you have the money, just station one noctis at all your mission hubs, shouldn't be more than 2 or 3. You can run lvl 4s in the Misha area for Amarr and Minmatar, maybe more?
I did the 34j to Ordion from Rens quite a few times, just for some bay12 actions, and then back again.
Others regularly jump 2-5 Incursions ships through half of highsec to get them all to the new Incursion (now that would be too much for me as well).
But then, it never occured to me to salvage in a BS (ok, the ones I used had a maximum of 1 utility high).