I think it would be cool if balancing suggestions got a different forum to ideas, I'm not sure if Patrick wants this sort of thing here or not but whatever, he's free to shred or move my message as he likes
Anyway, I started playing The Protectors fairly recently and I really like many of the improvements but can understand some of the things you've encountered. Massive units like Giants are actually worse off against towers and projectile units than normal Orcs for example (1 giant with ~220hp vs 4 orcs with ~140hp each). The new unit balancing has brought on a whole range of issues to my mind, many of which to do with the heroes themselves. I do like that the basic units have been brought up towards the advanced units and heroes, but few initial changes to the heroes means frailer classes end up being weaker than a single basic melee unit. Whenever I'm playing, I tend to refrain from sending my hero across the map even with a reasonable army in tow just out of fear of getting one-shotted. As the basic units have been empowered, more advanced units have taken a massive toll and the towers have been buffed. This presents another problem to the game, as towers are now so powerful that they'll easily be able to kill any hero in one or two shots. If you're marching your hero around at the front of an army into the fog of war, you could end up instantly dead. In essence, all heroes need to start off with much more hits, armour and resistance just to survive a shot or two.
I think a good resolution is to either have resurrectable heroes and/or follow what Warlords Battlecry 1 did and make all heroes roughly equal upon start (they all started with around 300hp, even wizards). A long time ago, I asked Faestus/ESPee if he could create some sort of repeatable research at each HQ building which resurrected dead heroes. The reason behind this was because the loss of a hero essentially ends the game for the player. I think the new ability would kill two birds with one stone so to speak, because this would also solve all forms of the Assassin and even unexpected insta-kills from stuff like towers.
The equalized units in general make pretty much all units which cost more than 1 unit cap questionable. I've never refrained from producing Minotaur Kings before in WBC3, but 4 Minotaurs are just so much better it hurts. Races with 2 unit cap-costing basic units have a significantly harder time dealing with other races. Their units, such as the Stone Golem, are approximately the same as other basic units but for every Stone Golem, the enemy has 2 of their basic units. I think that equalized units also take away a lot of individuality from the races. Bringing their stats up a bit is fine, but they should feel more unique and special in my opinion.
Tower vs unit combat is generally extremely virulent, where towers butcher anything they come across unless the enemy has reached them in which case it's the other way round. It's fine as it is, but I'd prefer it if towers stick around for longer and were less abusable. Tower stacks usually make defence so much stronger than offence just because they kill anything before anything can reach them. This is a problem with just about all versions of Warlords Battlecry though, to an extent.
Catapults have provided problems since... ever, really. In pretty much all of the WBC games, catapults have been undercosted giant-throwing machines of mass destruction. The empowered basic units do a lot to counter this problem, but the Catapult's newly increased defences can still provide an issue. There are too many instances of games I've had in past game versions where all I or the AI had to do to win was spam or even rush Catapults at the enemy. However, they're absolutely essential for some races, which can't really do anything with any of the units they've got against the newly buffed towers. The AI really love creating a massive bulwark of those things, and games can occasionally last forever due to them. I think buffing the Catapult's damage to 60 and making them do half damage to units would do the trick.
Another thing I'd like to bring up is the Aristocrat vs Plutocrat perks. In general, the latter is always going to be better because actually getting the unit is nearly always stronger than producing it faster. Saving like 2/3s of unit production resources is a bit mad. Every time you produce an Orc for example, you essentially gain 60 Metal at the cost of waiting an extra 18 seconds or so for unit production (something like 10 secs vs 28 secs). All those extra resources can then be used to create a much bigger base than the Aristocrat, produce more units, have more units out at any time and defend the base with more towers. Merchants from most versions of WBC3 tend to replicate this problem, where their value increases from simply existing (due to Charisma and skills like Wealth, Smelting, Quarrying and Gemcutting).
Sorry about the wall of text and hope this helps whoever somehow has the time to read it