I really don't agree with... almost everything said by the OP.
Let's see...
1 - I really don't agree.
My main solo campaign have : an undead shadowblade (dual-dagger, scoundrel, necromancer), the physical damage dealer. Sebille as a warrior (sword & shield, pyro, little bit of geo), doing both physical and magical damage. Lohse as an enchanter (hydro, aero, little bit of summon and necro). Nothing more, doing magical damage. I have no problem with the armor system : my undead takes care of mages, Lohse takes care of warriors and Sebille assist the one that needs it the most. The only troublesome fights were against Adramalhik, Mordus (mainly because I was underlevelled and with poor gear), the Eternal in the coffin (forgot the name, same reason than Mordus) and Alice. I stumble in some fights where I get obliterated from time to time, but some planning and strategy allow me to overcome them easily. The problem isn't armor, but strategy : you must use highgrounds and positionning.
2 - As said, my Lohse is an Hydro/Aero and she fares well in the damage department. She does more damage than my pyro Sebille, since Sebille has a Warrior build and, as such, no intelligence investment. Damaging abilities aren't numerous but I can manage... Even if the ennemy has armor, I uses damaging combos : wetting opponents with rain and ice totems befor casting hydro and aero damaging spells do wonders. As with the Armor, use tactics...
3 - Magic damage on physical weapons is far from useless : I ALWAYS put a fire run on Sebille's weapon. Why ? To ignite flamable surfaces. I always put an air rune on Lohse staves, to electrocute blood and water surfaces. From damage perspective, magical damage on a physical weapon isn't good, but it has its uses. Same as before... strategy, my friend.
4 - Again, wrong. My Loshe has a mediocre physical armor (even with masterwork runes) but she stands proud in the middle of a large electrified water puddle. Opponents wont rush her as often as they would if she wasn't. And she can stand in hazardous zones thanks to her insane magical armor... Add to that the skill that allows her to spend less AP to cast spells if standing in the same element, the ability to teleport opponents somewhere else and this is full of win.
5c - Perseverance, my friend. It does exactly that : restore some armor depending on the control affecting him.
Stealth - I can agree to what is said yeah.
Two-handed vs single-handed - As said, my Sebille is a sword and shield warrior... She is far frome useless, even without taunt on : she survive fights but can't prevent opponents from damaging my fragile Lohse ? No problem, she is loaded with resurrection scrolls anyway... She can't do damage ? Wrong... Tossing shields does a lot of damage and bounces. That said, I agree that two-handed weapons do too much damage compared to other weapons. This, in my opinion, is why you feel everything doesn't do any damage. Two-handed weapons are a no brainer and if you takes the habit of using them, you forget how to be a tactician.
Main features - Again, I disagree. Sure, two-handed do insane damage, but "sacrificing" intellect for memory isn't a loss... because what you loose in damage, you gain in versatility. My Lohse has a lot of spells, teleport others, heal, grant magic armor, control zones, shock, stun, chill, freeze, summon totems and so on... Tactical possibilities is what makes fights interesting.
Your view of the game and its problem is interesting because it reveal what you are looking for : damage, huge damage, killing opponents quickly without too much thinking.
I do not use two-handed weapons (apart from staves) BECAUSE it does too much damage. I like interesting (not necessarily difficult) fights. If my opponents drop too quickly, I cannot enjoy tactical planning.
In the same vein, I think AP is fine as it is. Conservation of AP, haste spell and tactical retreat makes a difference. More would kill such advantage. In my current lone wolf summoner gameplay, the AP augmentations is an incredible advantage in istelf... Sure, it's cool to be overpowered, to kill everything before it has time to react. But it's not that interesting...
For me, the only real problem, apart from the stealth costing too much AP, is the amount of damage two-handed weapons deal. But that's it : two-handed weapons deal too much damage, not the other way around - as in, everything else is lacking.
This. And summonners are insanely overpowered.