You symbolically win some kind of award for these post. Thanks for taking the time to write it all so thoroughly.
As we (I and a couple of the other team members) were reading these posts, we couldn't help, but bite our lip a bit thinking "Geez, I hope these people aren't waiting for updates coming out with all these changes". I am a little bit conflicted. On the one hand, we really admire and appreciate this input, because it's not impossible that will we release a patch and some updates to M:R, but it is unlikely that we will make some of the whole-sale changes you've brought up in your post. Furthermore, the chance for changing actual weapon models and art is very close to 0. The updates and patches that are likely would be things like map updates/additions and MAYBE some code/script adjustments, but by and large, M:R 2.0 with the MP Fix is as close to a final version as you'll get. It's also possible that if we do put out a patch, we'll roll all the last few changes into a 2.01 or some such. I'm not telling all this to discourage people though, and most certainly not to discourage someone like you to so throughly write and analyze our labour. I think it is fantastic that you are not only doing that, but having enough fun with M:R to pay such attention to all these details we've worked so long on. If you could only know the many times we've worked on little touches that we thought nobody will ever look at twice, but it's times like these when we find it worth the time we took.
I'll address some of the things you've brought up in point form, to try and shorten this:
1. The shotguns were not part of the original M1, so us adding them in gave us a bit of flexibility to what they would look/feel like. Hence, the differences between the M2 version and ours. It's still a kick-ass weapon with a bit of M:R uniqueness.
2. The ammo pickup/model differences is probably just an oversight on the part of whoever worked on the KKV at the time. It's unlikely this will ever change, and will probably remain as one of those interesting trivia factoids haha.
3. The flamethrower flame will probably never change. I think the programmers now would probably have the know-how to adjust it and make it a little more fluid, but I don't know that they will ever revisit it. The sound-looping MAY get fixed, but I don't know..same with the 5 vs. 7 seconds.
4. The SPNKR model may have a bit of Halo influence but it would have been incidental. In fact, the SPNKR was one of the first weapon models ever made (probably late 2000, if not Jan/Feb 2001), and we even re-did the whole texture for it after that. I remember the final Halo SPNKR model only being seen much later, and we even quipped about how close theirs resembled ours.
5. The alien weapon for everyone with the exception of the programmer (who probably toiled on it themselves for a while) was one of those things that as soon as we saw it working the first time we thought "wow, that's it, case closed." We liked it right away and I don't remember doing much adjusting at all for it.
6. Like the shotguns, the Pfhor staff wasn't something we had to include, but we did mostly as a nod to Marathon:Evil and Frigidman. Overall, we stayed pretty true to the feel of the original, and it's a nice little change of pace to use it through the game without the stress of lack of ammo.
7. The fusion pistol that you mentioned in the previous post went through MANY changes and adjustments. At one point, it was easily the most powerful weapon in M:R and we had to tone it down quite a bit. Even the fusion sprites were re-worked a few times. Next to the MA-75, the fusion pistol probably got the most attention, weapon wise. It is a shame the charging-beep doesn't gradually get louder, but it's likely not going to change now.
Again, thanks for the thorough post, and enjoy M:R. It really would be great if some of you guys managed to meet up for some MP M:R games. It's a lot of fun, and I think most of you are missing out on a great little experience. 
