Mitchell, I'm struggling to ascertain how computer literate you are, so I apologise in advance if I inadvertantly patronise you.
The work drunken coders have done is perhaps somewhat more complex than you realise. Digital Paintball 2 is designed to run on x86 hardware; it is created to run on processors which implement the x86 instruction set architecture. This is because Quake 2 was designed for these machines. When you write a program in a high-level programming language, it is computed by a compiler to generate Machine Code - code written in instructions that are part of the processors repertoire that is executed directly by the hardware. Obviously, this means that compiled code is intended for specific hardware.
The Nintendo DS uses an ARM7 RISC processor - RISC being an abbreviation for Reduced Instruction Set Computer. This is a different architecture to x86 and implements different instructions. Therefore, you can't simply execute native x86 code on the RISC processor.
Now, C/C++ code can be compiled for ARM7 processors; however, there are a number of things to take into consideration - such as that many program optimisations are made by finding elegant optimisation solutions in the assembly code itself. C/C++ allow low-level control of the assembly code where - if you are familiar with the instruction set you're targetting your code for - you can use intelligent substitutions for more efficient or faster instructions. Obviously, all these optimisations will have been carried out for the x86 instruction set, not the ARM7.
It's just not as simple as recompiling the source and packaging it up in a homebrew NDS. Some of the built-in functions and operations of C aren't even directly translatable to ARM7 (specifically with respect to dealing with floating point arithmetic, I think). The Drunken Coders guys will have put in a LOT of effort to get this to work, even without the absolute nightmare of the restrictions that the DS imposes. The point of all this being that it would be a huge amount of work to get DP2 running on the DS.
Also, consider that DP operates heavily on user-generated content - most maps you play on a daily basis were not shipped as part of the redistributable released by jitspoe. This means that maps are not federated in terms of size, processing requirement, texture use, custom texture size, any other required materials (sounds, models, skybox images, etc...) which means that most of the content associated with DP would simply be too much for the small resources at hand. I can think of very few maps that are popular in the DP community that are as efficient and conscientious as the original Q2 maps in terms of design and performance.
All this, and not to mention everything Eiii, Justinph5 and Zorch said about the desire to actually put the work in. Jitspoe will not release the source code for DP2 to protect the cheat-detection and other capabilities of the mod, and without it you could never hope to realise a DS conversion.
You seem like an enthusiastic contributer at least, why not get into mapping or coding and treat the community to some (slightly more feasible!) innovations of a different kind.
On another note - I was also impressed with Metroid on the DS, I really liked the controls and found them to be pretty intuitive. I have to agree with Eiii on them not being quite right for the prevalent gameplay style of DP, though. I don't think the Slot-2 expansion homebrewers market is large enough to really warrant the amount of work required by this mod, and the creators pretty explicitly say you NEED the GBA cartridge with 16MB of RAM. This also rules out your idea of the guitar hero controller to expand the control set too!
Hope this helps, anyway.
- Dag
P.S. jesus, what a lecture!