Best vehicle for the Mogul & Titan crate mission is the Buzzard, because hovering is much better (to stay behind the Titan with the Mogul, you practically have to stall a couple of times or circle around a lot, I've done it a lot) and the Savage's explosive cannon has a real chance of blowing up the Titan by accident.
As inconvenient as it may seem, use supply vehicles during certain ones, for example the Starling supply mission where you have to bomb targets, it is generally much better to use the resup Starling (as it has infinite bombs and is generally one of the best bombers in the game) than a Lazer (because it's a fast plane and you can smack into the ground, wasting tons of time) or Hydra (both jets have a low resistance to bullets, and blow up in one rocket. The AI have tons of RPGs during this mission and fire them off pretty sporadically. The Hydra also has a chance of you getting shot out of the cockpit, again wasting time). If you want to use a PA, use a SR vehicle for this mission (one of the new planes/helicopters with installable bombs, flares, rockets and guns, plus upgrades).
A mission where it'd be generally better to use either old jets would be the Molotok mission or the Nokota mission, provided you are fine with evading sh*t tons of missiles or you can get behind them w/o getting shot. I recommend the Pyro for this mission personally.
Generally, in most resupplies, aircrafts with bombs installed (infinite bombs) generally have a better reason to be used than most resup aircraft. For example, during the Seabreeze mission, it's better to use it because the bombs are infinite and there are targets on the water which will likely have crates in them (where it'd be better to use the Seabreeze, as it's ampibious), or on the land, where ground is an issue and you need a small vehicle with crash resistance (again, the resup vehicles are buffier than the OG aircraft). I'd preferably use a PA SR aircraft for this run, even though you don't have infinite bombs, the flares in a public session are a lifesaver and the aircrafts are much more buffed up with full armor than resup vehicles (I believe they have around 60% armor, might just be me).
Another mission I could talk about is the Hunter resupply. Use the Hunter, it's the best aircraft for this run. Either that, or use a PA Hunter, preferably the PA, as the regular Hunter doesn't have explosive cannons.
I'll end this off on any missions where you have vehicles with crates in them. Blow them up; it won't destroy the crates and you can pick up and carry the crates yourself, allowing you to use a vehicle of choice. This is a god send where you have crates in a unarmed Buzzard or a Boxville (or you are using the sh*tty Mogul during the start-up of the Hangar, blow it up and use an Akula in a full session. The Mogul doesn't stand a chance at all).