The FASS 150 and Airdog are good systems. This has been hashed over again and again on this site for the last 7 or 8 years, and as a general consensus, the stock system sucks. The in-tank option (as stated earlier) is better than the original system, but is still limited to "Stock" applications. Some individuals will argue to the ends of the earth over which pumps are good, and which are not. I can not make the decision for you, but only base the following on my own experiences and my research.
Going with the aftermarket systems is great for the stock truck, but will not gain any HP or MPG. It might, at best, extend the lifetime of the VP44 (but many factors contribute to this, ranging from fuel to operating conditions and drivers). What I have not seen in this thread is the reliability of aftermarket vs. stock. Anybody saying anything else is trying to sell you parts, or is just not informed.
Yes, an aftermarket costs $600+, but I almost guarantee that you will never need to change the unit. I personally changed 8 stock lift pumps on my truck in the first 2 or 3 years of ownership. I could not take the pumps to the dealer for warranty, as I voided my engine warranty with mods about 1 week after buying my truck. Since then, I have put on 2 FASS units (I had some gasket issues, one of the original blue FASS units, very rare units, only about 100 made) on my truck, and countless units on other trucks. I repaired the original, and it is now sitting on the shelf as a spare unit. The FASS 150 (with filters) has 3/8" lines, and is good to 500hp. I had to upgrade mine to 1/2" lines with a 1/2" pickup in the tank because I could actually pull my FASS down below 12PSI (from 17) at WOT.
I have virtually every aftermarket thing on my engine that you can imagine, and the FASS runs great. With the 1/2" lines, I can not move the FP gauge from 17psi, no matter how hard I push on the loud pedal.
As far as I am concerned (and I am certain a few others here would agree), get rid of the stock fuel system. At a minimum, eliminate all the Banjo bolts, move the fuel pump back near the fuel tank,and get a good mechanical fuel pressure gauge from 0 to 30 psi. Even the stock lift pump back near the tank will work on trucks with minor HP mods, if the pump is utilized in a fashion where it pushes fuel, not pulls fuel (again hashed many times here over the years), it should last a little longer, but it will eventually fail (just not heavy duty enough to push that much fuel that far). Many individuals on this site have performed this mod, I think they have spent way more money in the form of time engineering one of these retrofits than the aftermarket kits cost.
Before D/C began using the in-tank pump, they had a retrofit kit that lowered and moved the lift pump back towards the tank. It was not a popular conversion, but there was a wire harness and bracket available (although I think it did not do anything).
I would not really worry about air in the fuel. Any time that the fuel is pumped, you create a turbulent flow, with air pockets in it. I do not care what kind of pump you use for this, or what type of system you have. Some pumps control this, and attempt to provide a more laminar flow, but there will always be air in the fuel.
The more important thing here, is sufficient volume (something like 70% of the fuel is used for lubricating and cooling the VP44, and is then returned to the tank) and pressure. Insufficient volume, and cavitation will occur, run dry, and eventually burn up the internals. On the older pumps, with the brass plungers, this happens sooner than later. Since Volume is only slightly related to the pressure and the diameter of the fuel line (using some calculus), we can infer that a certain pressure, say 10psi equates to some specific volume.
Insufficient volume or a lack of pressure can eventually lead to premature failures typically indicated by hard starts and/or rough running at first, or can simply flat out fail. This can be tracked down to a few specific items within the VP44, most of which are mechanical. If you search on this forum, you will find a few people who have rebuilt the mechanical portions of the VP44. There is one thread somewhere out there that has great images, and explains one of the primary mechanical failures very well. If it is an electronic failure, it is just easier to replace the pump, as tracking down the component that has actually failed on the board is nearly impossible (even if you figure out what is damaged, if it is a EEPROM, you will most likely not have the software or tools to re-flash the chips).
Unfortunately, very few shops are equipped to properly diagnose what is wrong with a VP44, and even fewer are able to rebuild one. Trust me, the local Dodge dealer is not on the list (neither is Mopar). I used to work for Daimler Chrysler Rail division (we are now a different company). Chrysler does not have the facilities to rebuild these units, nor do they care to. They simply buy new units, then put on a 40% margin and retail them. BTW, 40% was the standard margin for any part. If anything came in the door ranging from terminal blocks to a circuit board, it got 40%. This 40% was incurred at each sales point, even internal sales to different divisions, which is why some parts, like mounting hardware, costs 500% more than at the autoparts store.
For the amount of money that is spent on installing lift pumps when including the labor to install, you might as well put on a unit that will not break as easily.
If this forum is searched, I would be willing to bet the most popular item in the 2nd gen 24valve area are items related to Fuel Pressure, VP-44 failure, and lift pumps.
And one other thing that drives me nuts (me being an engineer that has to be correct). It is not the sulfur that is the lubricant in Diesel fuel. Sulfur is not a lubricant in of itself, but it can combine with the nickel content in many metal alloys to form a low melting point eutectic alloy that can increase lubricity.
The process used to reduce the Sulfur also reduces the fuel's lubricating properties. Lubricity is a measure of the fuel's ability to lubricate and protect the various parts of the engine's fuel injection system from wear. The processing required to reduce sulfur to 15 ppm (ULSD) also removes naturally-occurring lubricity agents in diesel fuel. You can find much more from Chevron and Wikipedia.
A good water separator filter will get rid of any minor/trace amounts of water in the fuel, if they are maintained. If you have a tank of water, no separator will help with that, nor prevent damage to any of the VP44 (or engine, remember, liquids are not compressible, and are significantly more powerful than the head gasket/studs). The stock filter/separator is OK, but is not designed for high-mileage trucks, or fuel-hungry trucks. A good Fleetguard aftermarket setup would be better. You can also get better Micron rating filters with an aftermarket setup.
These are just my $0. 02, but if you want something reliable and would like to make every effort to maximize the life of a $1100 VP44 (4k was a rip by the dealer) get a FASS or some other aftermarket fuel pump (get one with good filters).