Nice list of balance complaints. I think your factual statements (such as "tanks fail to break infantry lines") are mostly true. But whether it's a bad thing or not is more subjective, and sometimes fixing a perceived unit balance issue can be more damaging to the actual gameplay, which is not first and foremost about unit vs unit counters. I think some rts games suffer from a preoccupation with unit vs unit balance. About some units being useless- yes it's true that there are some units (tracker, ground flak, crawling bomb) that are mostly or totally useless. Is that a good thing? No, but the fact that they exist doesn't really hurt the core gameplay except by being noobtraps. And Pepe's done a great job the last couple of years of giving previously useless units some use (zeus for example).
1) Game too dependent on longer range units - You're not the first to have that opinion about nota, though long range units have been toned down a bit over the years. The general theme in nota is that longer range units beat shorter range ones, but at the price of decreased mobility and more vulnerability to air. So it's map and situation dependent. The more quickly frontlines become gridlocked, the more of a role will be played by long range units. Snipers do win against thuds in an even situation, but not if the thuds are on a hill (as you discovered). Terrain is more important than army composition in nota. You usually need to either wear them down first with mobile arty/air, or outnumber them enough to make storming the hill feasible- spy bot emps are useful in these situations as well.
2) tanks against infantry lines - Yeah, I think it is true that in the mid-game, once there are large infantry lines, tanks tend to become secondary. In the early game med tanks and panthers are really useful because of their speed and ability to take hits and flank, but the only tank that really is effective against large kbot lines is the goliath. It might be interesting if medium tanks were slowed down somewhat while being buffed in some combination of weapon firepower/aoe/range to scale up better in the midgame against bots, while light tanks could be adjusted to take over part of the current early game role of medium tanks. At the same time, I think the current balance is pretty good, even if tanks do become a bit obsolete in the midgame, and it's a tricky thing to mess with.
3) artillery accuracy - Yeah, that is a sort of inconsistency that I guess is sort of a carry over from OTA. Thuds, morties, plasma batteries, oddities/galas have excellent accuracy, while mobile arty, ship guns, vehicle t2 rocket arty do not. Nevertheless, that's how the game is balanced and it makes different arty useful for different things. Mobile arty and t2 rocket arty are inherently offensive in nature, for wearing down armies/defensive positions, while the plasma battery style weapon needs its precision to be useful for stopping mobile arty creep.
4) Agreed that ground flak is useless in current version. Pepe is buffing them in next version though. Slashers/Samsons are very good though. Kbot t1 AA aren't great because of limitd range, but they do good dmg/cost. Razorbacks are pretty good.
5) T 1.5 overpriced - Yeah, it's true that these units aren't worth building in a serious game.
6) Mobile bombs - They're mostly useless, but not entirely. 1) mobile mine (they burrow/cloak when stationary) 2) load on transports and self destruct transports over an enemy building/shipyard or something. Also, Pepe buffed their speed for next version.
7) Fast bots - There are a few rare situations where I've found them useful, for example, fighting hovercraft artillery on land (which can skirmish pretty well) or raiding lightly defended mexes on open maps when the enemy doesn't have precise ground attack planes (vashps or toads). They're an exception to the general rule that kbots are slow but cost effective, which means they can't be too good or the rule wouldn't exist anymore.
8 ) Ships too high-value - Well, that's what naval combat should be about, in my opinion. In contrast to the land game where the key to winning is taking and holding territory, in the navy game the key is building up and not losing your navy power, particularly your big ships. I enjoy the tension it creates, like walking a tightrope where you have to balance caution with the ability to recognize and take advantage of a favorable situation, making decisions that can win or lose you the game oftentimes with limited information odue to the prevalence of jammers and heavy AA that makes scouting harder. It feels the way a naval strategy game should, in my opinion. However, I do think the naval game is hurt by a lack of good, sufficiently open maps- the only one that I really like for the naval game is expanded tropics. On small seas like the one on tempest, I agree that the all-or-nothing nature of the sea game doesn't play well.
9) Napalm bombers - I had a bit of trouble too the last time I used these. They sometimes have trouble bombing with hilly terrain because they fly so low and fast.
10) Bomber fuel - Fuel in nota is an abstract conglomeration of actual fuel and ordnance. I think it would make things unneccessarily complicated to have both seperately.
11) not enough high-alt missiles - well, if you really want a high alt missile on land you can always build a krogoth
12) Rocket box better than sabot - yes, rocket box is better overall, thought they don't really fill the same role. why should every unit be the same as its counterpart in the other faction?
1b) AA unpredictability - Flak units have a slight limitation on their firing angle so that they can't shoot really low flying (napalm bombers, gunships) or parked aircraft at a distance, or damage ground units. It does make them unable to shoot planes below them when placed on a tall hill.
2b) can't shoot units in wrecks - units were given avoidfeature tag many years ago because of frequrent problems with lasers and other weapons stupidly shooting at a unit they couldn't hit behind map features etc while ignoring units they could hit. Neither alternative was ideal, but it seemed the lesser of two evils.
1c) tank rear armor - If you're talking about real tanks, the panzer iv h had 80 mm front glacis armor, 50 mm front turret armor, 30 mm side armor, 20 mm rear armor. 30 to 20 is a pretty significant difference. In the game, the big penalty for rear armor makes retreat micro bad. If you're not careful in early tank fights you can really get behind if you get in a bad fight and can't get out of it without exposing rear armor and putting yourself at an even greater disadvantage. Maybe that's bad in some ways in that it makes things more unforgiving and hurts the player who's already losing.
2c) configurable unit states - that would be convenient and nice to have
3c) armor types - It's actually really simple and pretty consistent, it's just not visible to the player anywhere which it probably should have been. The thing to understand is that "armor type" has NOTHING to do with the armor flanking bonus/penalty that tanks get- they're completely unrelated. The majority of units are all in the same "light" armor type. The others (all tanks, zeus, large t2 kbots, t3) are in medium or heavy armor. Medium and heavy both give good dmg resistance to light weapons (red lasers, emgs) and moderate dmg resistance to non-armor piercing weapon types. Armor piercing weapons are rockets, gauss, bombs, annihilator type lasers, and high-damage, low aoe shots (reaper, bulldog, indian). They do full damage to all units, regardless of armor type. Heavy armor is just a more extreme version of medium, and takes very little damage from light weapons. Protip: the color of terrain of a unit's buildpicture indicates whether the unit is armored ( either medium or heavy) or not. If it's on desert terrain, it's armored, if it's on grass, it's light. Again, this is not related to the flanking armor bonus that tanks get.
Looking at your complaints as a whole, you seem pretty focused on unit counters, which isn't really what nota is about so much. Games aren't ususally won by producing unit x when opponent makes unit y. Yes, army composition does matter and can make a difference, but as long as both players are doing something reasonable (ie not something stupid like leveler only spam), the game will usually be decided by other factors. What you build does matter, but as much in relation to what terrain they end up fighting on and the status of the frontlines where they're fighting (open vs gridlocked), as the type of unit they're fighting against. nota is less about rock/paper/scissors balance and more about army positioning, allocation of forces to different fronts, and finding a balance between the different branches of your forces (kbot vs tank vs air) that will win against what the enemy is doing.