Personally I like the Paradox merged mods since they reduce the plugin count and, perhaps more important, are more up-to-date than the original plugins. They often have fewer unclean records (ITMs and UDRs) than the original plugins. If you are writing compatibility mods like Blackened it's a lot easier to write for the merged versions than to have to maintain multiple versions of the patch, and I've been using Blackened patches because they are being maintained and are updated when needed. The one-size-fits-all approach in Paradox has problems with Enhanced Blood Textures, but I haven't seen any other significant issues. You can see the Paradox mods I'm using in the STEP Fallout 3 guide listed in my signature.
I've looked at FOOK and I prefer FWE; FWE also has a lot wider support which is particularly important.
Ghostwise has been also been working on some FO3 patches, and has what seem to me to be a nice scheme for organizing the patches. It seems consistent with the approach that ElminsterAU described in this forum thread about how patching could be made easier and how the next release of xEdit will support this (ModGroups). I think it's also compatible with your goal of having patches for various mods that are compatibility for FWE, WMK, EVE, RH_Ironsights (when feasible), and all the DLC. The only difference might be about having one mod for all the weapons of interest vs. having groups, and eventually with ModGroups it should be possible to more easily merge the individual patch mods.
STEP recently moved some of the discussion about xEdit (FO3/FNV/TES4/TES5Edit) to a new forum on the site. You'll see it under Support and Troubleshooting. The Bash Tagger thread has a lot of information on using xEdit scripts and the new beta xEdit, and includes posts from a number of the key modders working on useful xEdit capabilities.