Depends
Hello Aaron, the pros and cons concerning upgrading an auto trans vs converting to a stick are many and really depend on whether you are going to pay someone to do the conversion or if you are very mechanically inclined and skilled and can do the work. Just how much power you want to have and what you use the truck and added power for [towing, sled pulling, drag racing, daily driver etc] play a big factor in the decision too.
Matt is an extreme on the side of being mechanically inclined and skilled. He will take on a new project and get it done or at least operable in the time most of us just start to form a plan. But he is an exception. I also don't think he sleeps much!!
If you are able to get a donor truck, and can do the job yourself, then I would say that this may be the best way to go. But if you are paying someone to do the work then I have to say forget it. You will have as much or more in the swap than in an automatic upgrade.
And unless you do each and everyting to turn the truck from auto to stick, including the speedo cluster, steering column etc. the truck will always look like it was 'hacked upon' and unfinished. And resale value will suffer greatly.
An upgraded auto can handle pretty much any power you want to apply through it. If you want to say the same thing about a stick shift, then you have to do the input shaft, upgrade the fifth gear and shaft, and of course buy and install a premium clutch [$$] at the same time. Then and only then are you equivalent to an auto trans with all the proper upgrades.
If you are in the Michigan area, I would encourage you to contact Matt, and see what he can show you it took to do the job, then contact me and let me show you what goes into a good auto transmission. Then hopefully you will have some extra info to make your decision with.
Hope this helps, Greg L