Heavy Cannons are kinda bad. In fact, most 'heavy' weapons suffer from sniper rifles occupying their niche in addition to sniping. The Auto-Cannon might be somewhat useful as a HE/Incendiary dispenser, kind of like a direct-fire grenade launcher.
Kitsune should be your top priority. Abandon everything else and put all eggheads on that, pronto!
15 Osiron crates might be a passable trade for a semi-vet, depending on what you get from them.
If you like the Skyraider's side doors, you'll love the Skymarshall. And perhaps also the new Lightning, that thing is like a giant turret in ship form.
Some of the Syndicate guys should have been in their variant of the Armoured Vest, too, no?
About the African base, depends on how much science infrastructure you already have. But since you're regularly losing people, I'd make a training base
somewhere anyway, so why not there. Research takes a while to set up, though, so if you want both, start with that.
Teaching your agents Ninjutsu is perhaps the least accessible of the main four transformations. You need 'gym max' in several stats, some natural psi ability, and a bit of actual melee experience on top of that. I think commendations can help with stat requirements, but earning those commendations will usually yield the necessary skill increases by itself.
Did you mean Bulletproof
Coats? Bulletproof
vests are Kevlar.
Name suggestions for the Rover are welcome.
Landranger?
I advise upgrading to Smart Rifles ASAP if you're still using ballistic rifles. These are the best general-purpose kinetic rifles in the game.
I concur that MiGs are pretty useless once you get the Kitsune. They might be of some use against cultist MiGs, Hybrid aircars and similar, but the Kitsune largely obsoletes them even in that role.
The Interceptor is something you may actually want, since the next crafts require alloys which might be in short supply. And not all UFOs land. But whether those are worth pursuing is a different question. I'd get one or two of one interceptor type, MiG or Interceptor, build spare hangars to move them around, and try them out. And then upgrade.
Once you feel the need to have something worthwhile in the air, beeline for Thunderstorms, those are IMO the best early-midgame fighter crafts.
Personally, I like to have a fighter craft in each base, but I admit this is not due to anyt efficiency concerns. I just like to play as 'proper' X-Com.
Taking down another cult depends on whether you care about stopping the manors and other minor bullshit from spawning or not. Since Hybrids will continue that anyway, and are somewhat tougher, perhaps not.
You'll also get those annyoing score-lowering Slander missions if you delay destroying the respective cults, so that's something to watch out for. Contrary to what Stone Lake is saying, destroying the cults isn't itself a pathway to new factions - usually, it's something you take from the cult's higher ranks or their HQ.
The exceptions are: Black Lotus (which is already down) - two mission arcs, EXALT (also down) -manufacturing certain somewhat useful items, Red Dawn - not really a new arc, but closure for an old one, Dagon - alternate access to the underwater arc if you miss your Deep One capture.
There are also some extra Geoscape events that give you minor penalties if you take too long.
All in all, I like farming the cults for longer, but if you're not into it and think you can handle Red Dawn snipers, armoured cars and
Deep Ones Gillmen/Dagon priests raining lightning, TNT and grenades on you, go for it.
Personally, I dislike the Ghost arc for not fitting well into the 'X-Files' environment, but that's just IMO. So I can't tell you much about it. It does have a bunch of pretty useful equipment for you to turn against both the Ghosts themselves and other factions.