I had a 98 Dak V6 Club Cab and upgraded to an 05 V8 Quad. I've debated several of topics that you mentioned and this is what I would say IMO...
1. V6 vs V8: No brainer, 100% def V8...MPG is minimal (if you really were concerned about mpg's you wouldn't even consider any kind of truck)
2. if you're planning to haul or tow anything more than once or twice a month it'll make a huge diff
3. V8's have waaaaay more aftermarket options than the V6
4. the V8 is just a sh** ton more FUN
5. I might be lucky but I live in northern Ohio and we get our share of snow and salt...as such I'm a bit OCD with not just keeping her clean but doing a clay bar in the fall and spring followed with a goood wax job and I've had *******ly no rust in comparison to just about any vehicle around thats almost 10 years old
6. a bigger bed would be nice at times...if I needed the length on a regular basis I've seen vids on people who diy'd a bed extension platform that would bolt into the bed/frame when they needed it
7. The extra cab space has been a blessing, granted I have a fiber tonneau that in itself makes the bed into a "trunk", but for weekend shopping etc, it's nice to keep my stuff where I have easier access (and somewhat climate controlled), been many times that I've traveled with more than just one passenger, if I had rear sliding glass yeah it'd be nice to be able to reach back and open/close it on the fly but with 4 big windows the air flow is plenty
8. Front suspension should be stamped "Made in Taiwan" (by degenerates), just do yourself a favor and don't go cheap when you do replace it...check the General Discussion area for "Deals and Steals", if you're a savvy shopper you can save upwards of 40% on most of the parts you'll ever need.
9. As Dak's are getting older, it's getting easier and easier to find junkers and clunkers that you can get parts from cheeeeaaapppp.
10. I'd love a big boy truck like most others, but aside from being able to find a killer deal when I might've had the means...about 1/2 of time I have to navigate or park in urban areas that can be a nightmare for even the more experienced bus drivers.
11. Again, maybe I've been lucky, but I've treated my lady with about as much respect as I can and have taken good care of her...so, other than a few check ups at the doctor, overall she has been really good to me right back.
12. Not familiar at all with the 6 speeds, but I'll try to post a link to a YouTuber named 6SpeedDakota. He has some pretty decent videos and if you were to contact him, I'm confident he could give you some very sound input on the manual Daks.
Hope this helps your decision making and regardless...in the end you're happy with whatever you decide to get.