1) Flame weapon
[snip]
Being able to deny your opponent cover is crucial. Grenades work to an extent, but aside from molotovs or incendiary grenades they're pretty easy to dodge and continue using cover. Flames forcing you to change up your opponents playstyle is what makes them tactically useful.
As for unequal distribution, that's fine too. Used to have such a discussion all the time in Dawn of War 2 and ultimately what it comes down to is that the factions are different. Brits only have the WASP (although you severely underestimate the universal carrier) for flame, but they have the best sniper in the game, base arty/mortar pit and can outshoot damn near anything from their own green cover. OKW have incendiary nades, ISG and flak weaponry.
Rifle Company is a special case, the flamers are actually the relatively balanced portion of the doctrine. Having early vet 2/3 and a generalist tank to fall back on are the real problem. I'd much like to see the easy eight swapped with the bulldozer sherman, but I doubt that would ever happen.
2) Indirect Fire Units
[snip]
Flank? Counter with your own indirect fire units? Honestly, these units becoming barrage platforms would make them pretty damn useless against anyone smart enough to move.
3) Weapon Upgrades in General
Upgrades are, well upgrades. If we had multiple weapons to choose from I'd agree with you (i.e mp40 upgrade for grenadiers) but we don't. Dawn of War 2 handled this much better since there were squads like Tac marines or weapon teams that had multiple options for upgrades, with the units role often changing entirely when upgraded. (i.e weapon teams upgrading to autocannon lost suppression, but did more damage against everything. Or they could get las cannons for strong anti vehicle) It's much more straight forward here, most units only have a single upgrade or with say weapon racks the option to pick anti infantry potential or anti vehicle potential.
In general, not spending resources should not be a superior martial choice as well as economic one.
4) Loiters (aka Skillplanes)
You don't need to AFK your AA unit, you know. imo the easiest way to tweak this is to fix these without simply removing them is to reduce the loiter AoE so that it can only really cover 1-2 strat points. And maybe tweak the duration/vulnerability of the planes a bit.
5) Abandons/Out of control
lol Nah.
Anyway, you have too much of a hard on for green cover infantry battles. I don't know how you can propose flame weapons being too good against cover and that indirect fire should be necessary and then go onto say that indirect fire should be a shortlived barrage. Cover should be important, but it shouldn't be a be all end all. Your stance reflects the game's long lived metagame of "build lots and lots of generalist infantry". The reason Rifle company is so damn successful is because if you try and fight outgun them with infantry you're going to get smoked. It's a damn sight weaker against support weapon play or vehicle play. (Or a mix of the two.)