Edit: I'd like to know what's next on your list. I'm dreaming of mods everyday
I mostly write stuff for the Piratez! mod by Dioxine. Once this is out, I guarantee you won't be disappointed.
EDIT:
I promised you I'd work on this mod further, right? So, let me present the next iteration! This one goes beyond simple retaining of low-level weapons throughout the game, as it adds a new weapon that aliens use:
Yes, it's an alien sniper rifle that the enemy actually uses. It can only be found in some missions (where I arbitrarily decided a sniper rifle would makes sens, for example in terror missions - city fighting). It lacks autofire, but is very accurate and a bit more powerful than the Plasma Rifle.
The sprite was made by Shadow (impressive job!) and somewhat modified by yours truly (mostly adding the sniper scope). I plan to work on the handobs a little more, but I think it's not bad already.
My next project regarding this mod will be a light plasma cannon which explodes on hit. I'll have to make it from scratch though, so it'll take me some time.
Download the enhanced version from the first post in this thread. If you want the basic version 1.0 (without new weapons), download it
from Jo5hua's mod site.