Keep in mind Emissions warranty is good for 5yrs/100,000 miles. I would go with one that is still covered under emissions for peace of mind. Of course the previous owner's maintenance will be more important than the emissions warranty.

Don't delete until there is an issue with the emissions, or out of warranty in my opinion. I know a few guys with 400k plus and no emissions problems, they tow constantly and that really helps to keep the dpf clean. A tank of def usually lasts an oil change interval.
Will deleting make it more reliable? Sure, but it's not that its unreliable stock.
On the other hand all the emissions equipment is only on the truck because of federal government mandates. Powerstrokes in non emissions compliant countries don't have dpfs, egrs, or def tanks. They also still have ashtrays and cigarette lighters...

The Achilles heel is water in fuel not too many dpf, egr, or def troubles.

Get a long bed, shot beds have a baby fuel tank. Better yet get a titian tank, or an auxiliary tank.

Use only motorcraft filters: oil, fuel, air. I found the best price on Amazon.

Get airbags for towing, I have airlift they work well.

Change out the plastic CAC pipe for a metal one.

I would caution against Amzone parts. Lots of China copies on there.

Wow I really appreciate it, this is the solid info I need, all the quirks and what it takes to keep her healthy/happy from an actual owner.

What causes water to get in the fuel? condensation? How would auxiliary tank help?

Most often water in the fuel is from contaminated fuel at the pump. Honestly the best way to handle this is have good insurance. My state farm agent said that I was covered.
A station that has bad storage tanks, that got flooded, put gas in the diesel holding tank, etc.
Condensation at the trucks fuel tank should be easily handed by the factory filter, the separator needs to be drained every couple weeks. A pint sample is good.
Diesel is also hydroscopic, it will soak up moisture from the air. Again not generally a big deal, if it gets driven.

An auxiliary tank will allow you to drive past all the sketchy fuel stations out in the middle of nowhere, load up on fuel when the price is down, pre filter all fuel before it ever gets to your truck's fuel tank. I just got back from a 1500mi round trip and had a quarter tank of fuel left. Passed all kinds of stations that where $1-$3 higher per gallon.

The main problem with buying a 2016 or older is that there's only around 2 or 3 Banks performance parts available for the 2016 model year (I own a 2016) engines, all that's available is a cold air kit and 1 tuner that has generic tunes which can cause more harm than good. I have had no engine issues, that might be because I don't even have 19,000 miles on it, I bought it new, right after it arrived at my local Ford dealer and was driven off the delivery truck.

For good highway MPG you'll want the 3.31 gears, I was getting 20+ mpg (@74 mph) with my 2 wheel drive F-250, my F-350 has 3.73 gears, DRW and 4 wheel drive, I'm lucky to get 11 mpg (@65 mph) towing my 5th wheel and 16 (@74mph) without towing. If you're wanting to put performance parts on the truck you'll want to get a 2017 or newer as that's the model years that the most parts are available for.

I can't tell you how the egr/dpf deletes will affect the drive ability or engine longevity on the 2015/16 model year trucks, but, I can tell you that deleting the dpf is a federal emissions law crime that carries at least a $2,500 - $5,000 fine per item, when/if you're caught, the same goes for the rest of the mandated emissions equipment installed on the truck.

Actually the separator is supposed to be drained at 3o day intervals, I don't understand why Ford didn't put automatically draining fuel/water separators in the superduties.

Couple weeks or 30 days your choice, I am willing to bet most dont drain it at all. I would bet dollars to donuts, but the price of a decent donut is outrageous.

Don't buy a 250 to tow a fifth wheel. If you want awesome mileage get a VW diesel. Dually is the way to go towing. I have gladly traded the 5 mpg for the safety/longevity/handeling benefits of a dually.

Banks can suck it(no offense). I would never put an intake, or any other air filter other than motorcraft in my truck ever. Economy of longevity trumps economy of fuel any day of the week, twice on Sunday.

Getting caught deleted and being charged with a federal crime would be a bad day.

I have to disagree with having good insurance as being the best way to handle this. The best way to prevent ever dealing with fuel problems is to put an additive in such as Diesel Kleen in to every tank of fuel. Rids yourself of problems almost immediately...and you won't ever have to deal with insurance, because I can promise that is always a nightmare.

A quality fuel additive like stanadyne or archoil is a good way to hopefully preserve the life of the hpfp, I don't hold much confidence in Diesel Kleen personally. It should help with long term wear. Especially if the additive has a demulsifier it will help control condensation in the tank. I have used all 3 of theses.
However the trucks I know personally that have >400k miles have never had a drop of additive in the tank.

If I ever get an entire tank of fuel from a station that is trashy, right full of water, or mixed with gasoline, I know that no amount of fuel additives will abate this problem. If someone puts 5 gallons of DEF in the fuel tank, fills the tank from the gas pump, or whatever is the same thing. It is this situation I WILL be filing a claim.