The DC skillup tweak was not implemented because it only affected a handful of people. There was a HUGE clamour over not being able to skill effectively as you leveled up post 85. The mobs they added in non-abyssea areas were not a large enough amount available to skill on. I know this personally because we went out to try to some of the camps and they were simply ovverrun with players--this was with a reduced population mind you, before the server merges. This was an issue that affected a LARGE concentration of the population. The first two fixes they tried didn't cut it for a large portion (not me, I was fine with hitting @300 in sky and finishing in Abyssea myself), so they eventually gave in and tried again with GoV. Haven't really heard much complaints lately other than the rarity of the skillup tweak from GoV. People are finally figuring out they can sometimes get a better skillup rate now on the weaker mobs and are starting to use that tweak more.
And yes, it did have a critical impact at large when the endgame content is requiring you to have certain weaponskills to be successful in completing that content, and people are struggling to get those weaponskills. The general cry they have been listening to is to make things easier now, and quite frankly it is starting to go a bit too far in my opinion. This idea is just another one of those things that is simply too unnecessary. I have already shown how in one particular example that was posed, having the chocobo in Mhaura would actually cause you to take LONGER to get to the destination than simply using the EXISTING METHODS ALREADY AVAILABLE.
In case you missed my earlier post, I listed well over 12 different mechanics (that's categories, like Abby maw warp is 1 mechanic, but you have them in 4 cities to send you to any one of 9 locations) already implemented to help you get around easier...and I think I left some out. I actually made up a list on a forum somewhere a long time ago. Forget if it was here or elsewhere, but it was a long list. If I can find it, I'll add it just for the contrast.
As for Nashmua, it probably wasn't added there because you basically are only running a cross one zone. Same thing goes with Qufim I guess (there is also the whole running through a long tunnel thing, which they've explained in other lore that chocobos don't like--they've had to "condition" the ones in Norg or something like that). Likewise, normally, chocobos would proly get too spooked in the caverns leading to Arrapago Reef and all. The other connected areas to that portion of the mire also have that indoor/underground classification so you can't use chocos in them either. So, it really didn't make much sense to have them their either. Probably the same logic was applied to tavnazia--essentially you are just running across one zone, and you can't take the chocobo into the neighboring zone. Chocobos are meant more for traveling long distances (ie, multiple zones, city to city, etc.), not just running down the street in comparison.