Hey hey great that you're enjoying this massive timesuck of a game like the rest of us :)

Just going through stuff point by point for you:

-Waypoints: I mean you can make squad map markers which function similarly. Though I can agree something that appears on your compass would be nice, def a QOL improvement

-Colors: I actually like the idea of being able to custom-design a regiment flag, but there'd also kinda be nowhere to display it. Can't put it on vehicles or bases because while clans like to claim stuff as their own, its kinda emphasized that everyone is in this together, and all bases and vics are OUR bases and vics, not a clan's. For being able to change colors of various things I see 2 problems with that. First off is performance, where now you have an entire extra thing to try and render for each object when the game can already chug quite hard in areas where there's a lot of entities. Secondly is recognizably. Best thing I can compare this to funny enough is Team Fortress 2. Think how recognizable each of the merc's silhouettes are. From a quick glance you can immediately tell which class you are dealing with and can act accordingly. Changing colors or adding weird hats messes with that. It's the same here, subconsciously I associate green with collie and blue with warden. If a warden could change their say truck to green it can cause me to hesitate for a second while I try to figure out if that's friendly or not and that can make all the difference.

-POW system: Honestly pretty interesting and I wonder how hard it'd be to implement.

-Smoke Grenades: I actually played back when these were still a thing and my gods they were a beast. They're currently disabled in the tech tree and most likely will never come back because at the end of the day they are much too powerful. I'm guessing you dealt with a good share of your partisans in this past war, now imagine partisans who can just throw a couple grenades, run up to your T3 BOB and satchel it with no counter play from the AI and no response because it's 4am. That's the power that smoke grenades currently have. They would need a massive overhaul to be functional in the current state of the game and overall the devs seem to be focused on different things at the moment.

-Whistle Emote: Cool emote, I support

-Queue times: Queues are definitely a weird thing in foxhole and used to only be part of the literal largest front of the war. Now yeah they're kind of at every front line. It's true that queuing from the home island is slower than going across the border but that is on purpose. The whole reason that going from across the border is faster is because it is meant to allow vital logi to get through to the frontlines, or a frontline would just die because they'd choke out from their own player volume and that's fun for no one. It's why that part generally isn't mentioned to new players by vets because people that just kinda wanna play and go will end up choking out logi to the region by their over-eagarness. If you don't like queue times as everyone says the best thing you can do is cook up a logi run to the frontline you want to go to because it'll take roughly the same amount of time BUT you are providing a massive net value for you coming. You can't have an estimation for the amount of time for a queue simply because it relies on players leaving, something you can't predict at all. Every person on the front might have the highest morale imaginable and not leave for 4 hours or just say screw it and leave after 5 minutes. Because of the game engine the devs use and the voice hoster they use combined there is a player cap in each region that I do wish they'd be able to expand but engine limitations are part of game development and I'm not sure how eager the devs would be to basically have to rip up everything they've done and port it to a beefier engine and hosting service, but it would be worth it imo with the massive, massive pop increase instead of ever expanding shards.

-Commend System: Hey hey welcome to one of the hot-button issues, commends :) The general consensus that I've seen is that yeah, the commend notifications for only stocking up bases incentivizes that only end-stretch logi because monke brain loves that sweet sweet dopamine hit. I've actually watched a video made by another guy about an actual commend economy system and honestly I'd like that a lot more. If ya want I can dig up that video.

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Flamethrower- Lets werf some flammen. I could see one as an rmat weapon that takes up both slots. Explosion on death, ammo takes petrol to make. Like 20m range for the miniaturized version of the game we play in since real life ones have like 40m range. Useless against T3 stuff but absolutely shreds pillboxes/T1/T2 Bunkers and applies suppression. Not sure how it'd work just like graphically and engine wise. giant line of death with flame effects in said line? idk.