Well if we wanted to mention the speed issue. in another TOS episode "by Any Other Name" we have an alien race that can modify Federation warp drives to traverse the vast intergalactic distances from the Milky Way to the Andromeda Glaxy to only 300 years. 2 500 000 / 300 = 8333.34 ly/year. If Kirk kept his word a robot ship would have been built. Which could have meant Starfleet gaining access to faster warp drives.
But as to the nature of the thread it's self. Any show has to follow the rules of it's it's universe. One could ask the question did Voyager stretch those rules to breaking point?
as for the torpedeo issue, yes there was a line re: That they won't be able to replace them. A simply change in the line would have solved the issue. "We only have 38 torpedeos and they will be difficult to replace"
Now you have changed from a definite to a possibility, you now don't have to say how you replaced them, because you said there was a possibility you could replace them.
Shuttles, Voyager could be possibly be described in modern terms as perhaps a destroyer (or at a stretch a light cruiser). So would a ship of that size have the facilities to replace shuttles. Perhaps it could have replaced one or two but the number it did, begins to stretch credibiiltiy.
Damage to ship, the most common argument is that they used the replicators to repair the damage. Which is possible but I suspect you would need an Industrial replicator to replicate hull plating. (Dialouge from DSN, seems to indicate that these aren't handed out like Candy, If memory serves the Federation gave Bajor 4, that's 4 for a whole [planet. So it's unlikely a small ship like Voyager would have one. Even if it did, it wouldn't have hurt to show the damage slowly being repaired over a period of episodes.
From TNG, I believe we were told that Federation ships use certain advanced materials that others races don't. With VOY it seemed the closer they got Federation space the closer in tech the alien races got. So finding those materials should have been harder in the earlier seasons.
The Beta Quadrant?
2374 -
Kes problems the ship 9500ly, ten years closer to home
Slipstream drive from the Dauntless 10 300ly another 10 years closer to home.
2375 -
Wormhole in void shortens journey by 2500 another 2.5 years closer to home
Borg Transwarp coild knocked another 15 years off their joruney.
2376 -
Tash Graviton Catapult knocked another 3 years off.
Factor into 5 years for ordinary jorney time
Total some 45 300ly traveled, leaving some 24 700ly to go or 25 years.
Size of Milky Way Galaxy ~100 000ly acrosss, I believe Earth is some 20 000 ly into the Galaxy. 20 000 + 70 000 = 90 000ly so at most Voyager was 10 000ly from the Galactic rim. As each quadrant it's widest is only ~ 50 000ly and Voyager was 10 000 ly into it, they should have been around 40 000 at most from changing quadrant. So 40 000 - 45 300 = -5 300 ly. Which should be the Beta Quadrant.
http://imagine.gsfc.nasa.gov/docs/ask_astro/answers/030827a.html