I have been wondering a few things:
Is it possible to create a transparent server mod that:
Can allow some slight modification to the original mod?
Can detect cheats based on what they are asking for and what they are doing with it rather than just a file signature type of solution as used by PB?
Or possible filter commands to what’s really required and nothing more?
Would anyone be willing to show me how to get something like that started?
Thanks
other than cheat detection, most of what you want could probably be accomplished with lua mod for etpro and cvar limits with pb or forcecvar
But other than doesn’t cut it and if you check my post again you’ll notice that I already have a mod in mind and BTW it’s not ETPro or ETPub and the changes I have in mind are pretty specific. 
Again, I’d like to address the AC with a transparent mod so it could be useful to any other mod, the rest is really optional, but would be nice to make some changes to game play for my favorite mod.
AC being the biggest issue in gaming today, I’ve been quite surprised at the lack of response on the issue, because anyone knowing anything about the subject knows that PB is a complete joke when it comes to cheating since it can only detect a cheats signature, which is trivial to change when you have the code.
I guess all the good coders are too busy writing the cheats to bother with an AC mod?
Not easily. Some mods allow customization, e.g. etpro’s lua API.
Can detect cheats based on what they are asking for and what they are doing with it rather than just a file signature type of solution as used by PB?
Or possible filter commands to what’s really required and nothing more?
You seem to be under the mistaken impression that cheats interact with the server in some different way than a human. In general, they do not. Some might be recognizably inhuman, but positively identifying them this way would not be easy or reliable.
Would anyone be willing to show me how to get something like that started?
You need to learn how the game works.
ftp://ftp.idsoftware.com/idstuff/et/sdk/ET_2.60_SDK_Setup.exe
ftp://ftp.idsoftware.com/idstuff/source/quake3-1.32b-source.zip
Once you’ve understood those, the answers to your questions should be obvious
I am sure those kinds of comments will get you all the help you deserve :roll:
But other than doesn’t cut it and if you check my post again you’ll notice that I already have a mod in mind and BTW it’s not ETPro or ETPub and the changes I have in mind are pretty specific.
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You could always write a completely stand alone anti-cheat solution that runs on both the server and the client. 
(John Carmack suggested something like that for Q1 when the source was released.)
Hmm… PunkBuster is real slack serverside. That means you can just basically hack anything serverside you want and change it, just basically load up another library and use some function pointers and you should be set. Clientside is another story, pb may give you some troubles, but as far as anticheat goes that shouldnt be a problem, as it would all be validated on the server anyhow.
It seems like most cheats are working because they are abale to get information, I assume from the server, in regard to the other players location, so the questions are:
Would it be possible to put some kind of filter in place to stop that?
If, so then why hasn’t anyone done it?
This isn’t correct. They use exactly the same information that your client does to display other players. Aside from perhaps inhuman mouse movements, a cheat generally doesn’t interact with the server any differently than a human.
Would it be possible to put some kind of filter in place to stop that?
No, see above.