Definitely not-fun to have to spec something that only applies to melee things when you're ranged, or in general:
Having to take literally the whole tree for just getting the central skill of it!

Yes, it is not uncommon in these games that you are required to "waste" some points to get something special,
but the current design of the skill trees is outright bad.

I'll explain "bad" in more detail:
Some tree has a central skill that is vital for certain builds (also called "build enabling" or so).
-> You have to take the whole tree to get it.
-> You can not vary anything in that skill tree.
-> No customization in that skill tree, no personal flavour, no room for ingenuity.
-> Everyone going for any build that requires that one skill needs to take the whole tree and has the same there as everyone else.
-> If something is taken by everyone (also everyone of a certain class or build), then this is considered bad, and in good games this is changed in a way that allows for variety even within that build or class.

The close combat tree is actually quite well designed, the only two issues with it is that it has an entire line that requires the target to be Slowed/Shocked/Stunned or Frozen. The other major oddity is that the crit reliant special skill isn't on the crit arm of tree.

The ranged combat tree has mostly just one odd spot, the ammo reload special skill being in-line while the overheat one is not is odd, if you are using a energy weapon it does nothing for you. It again has a line for Slowed/Shocked/Stunned or Frozen, which is not always the most useful (since many weapons offer no good way to get the debuffs).

The fact there is an aimed shots and execution tree, but not a heavy weapons tree is another oddity to me. Or that Aimed Shots only refers to Sniper-type skills and has nothing to actually improve the aim for normal shots (reduced spread).

Then there is the cap skills, regardless of if they are actually currently working, some are simply good while others are nearly worthless. As an example the Heat capstone creates a burn DoT when you crit (well it's supposed to). The physical one however at best takes 5 hits over 5 seconds just to stack to full effect, if you hit a different target (aoe/cleave/target dies) the effect resets and begins again. Personally I'd rather it change to a simple bleed + health regen stopper, then at least all the stuff for bleeds might be useful. The fact that only the axe causes bleeding is also rather awkward. Clearly sharp swords and chain swords are self cauterizing. 

The crit tree is another one with some special skills that the placement seems quite a bit backwards, swap the ranged(specific) for the suppression(general) one next to it. Same with the melee (specific) and Focus(general), also the +1%hp per crit (general) and the +5%crit for -5 damage reduction(choice).

Then there are a number of strangely specific or awkward trees. Execution is the first type, Damage over time is latter, in the damage over time tree one of the special skills causes engine and armoured types creatures to suffer +50% more Corrosion Damage. Except... what's corrosion damage? Then there is a bleed special skill that is linked off of a special skill to increase burn damage. Or the strangely placed and worded Fast Metabolism special skill, it's either a trap skill or it should really be in a different tree. By trap I mean it states the duration of poison, burn and bleed effects are halved, it does not mention on whom. If it is the ones I apply.. does it increase the damage to compensate? If it's the ones on myself.. why is it not in the HP or Defense trees?

Most of the trees could use a good rework, take all the conditional special skills off the primary lines unless they actually make sense to be there (crit required specials make sense on a crit line, ammo on a general ranged one much less so). Conditional lines should never be required to reach the capstone. There are tons of weapons that do not apply debuffs, so the fact that both the melee and ranged trees have an entire line that increases the damage vs enemies afflicted with those debuffs and that line is required if you wish to reach the capstone.. it's awkward.

I never see any build with Hit Point or Defense skill's tree maxed because the overall defensive passive are pretty bad.

The DoT sikill tree has so many bad passive and a global bad damage system (dot). Corrosion don't exit, that maybe poison... Because green... ? 

The perk who increase your burn damage scaled with your heat resist is badest than a simple node...

Yes the global skill tree system need a deep analysis and rework.

"Definitely not-fun to have to spec something that only applies to melee things when you're ranged, or in general:
Having to take literally the whole tree for just getting the central skill of it!"

You're well acquainted with ARPG, so name one (except D3) in which you don't have to invest skill points in lower bonuses (they are not wasted, you conveniently forgot to mention) to get major improvement

"Yes, it is not uncommon in these games that you are required to "waste" some points to get something special,
but the current design of the skill trees is outright bad."

As said, not "wasted" and you're contradicting yourself. Good point.

"I'll explain "bad" in more detail:
Some tree has a central skill that is vital for certain builds (also called "build enabling" or so).
-> You have to take the whole tree to get it.
-> You can not vary anything in that skill tree."

With 56 skill point on disposal, some skill-trees are a necessity. Taking other skills in tree to get to mastery or beta-skills is logical prerequisite - there are numerous bonuses from lower-skills and large one from finisher. 

Please show skill-tree that is usable and not imbalanced, and allow varying. I will judge it honestly.

"-> No customization in that skill tree, no personal flavour, no room for ingenuity."

Ingenuity in 56 skill-points. Please show... Also, I insist on 56 points, because game is in progress, it's current max and few skill-trees are a must-have. It won't be like that when additional contents is introduced

"-> Everyone going for any build that requires that one skill needs to take the whole tree and has the same there as everyone else.
-> If something is taken by everyone (also everyone of a certain class or build), then this is considered bad, and in good games this is changed in a way that allows for variety even within that build or class."

Soooo... If you're melee Crusader, you want to take no HP-skills, therefore avoiding something like 1000/1000 HP/Sup and various defensive/healing bonuse. To be honest, +10% for finisher is not even that important, in grand order of things. Some 10 points, however make melee characters life soooo much easier. And no, characters investing much in HP tree (and therefore not in others) miss some, get some (perhaps). This is a balance thing, and should be treated as such.