I recently beat Risen (third time, though I remember little of my previous two playthroughs).

I quite enjoy this game but I feel like some things were done worse than previous games (Gothic 2).

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First, the Soft-Targetting.

In Risen there's a kind of soft-lock on feature that lets you focus on an enemy and circle-strafe them. This is a helpful and necessary feature, but- Gothic 2 let you toggle a hard lock-on! Since you could toggle it at the press of a button it was ideal and didn't get in your way when you wanted to focus or switch targets. Sometimes the soft-lock gets in your way because you don't want to focus on a certain target, and sometimes it breaks seemingly at random. It's a real problem when your target switches in the middle of an attack-chain when you're trying to finish off a target and instead you just throw yourself in the center of a group of enemies.

Second, Proximity-Triggered Attacking.

In Gothic 2 you could judge when to avoid or block an enemy attack by the animation they made, but in Risen it's frequently the case that you're getting hit before you can even recognize that the enemy is attacking. Attacking seems to be triggered purely by proximity and either the proximity varies or it's really, really difficult to properly judge the distance.

The suddenness of attacks is the reason why shields are so wholly superior to dodging. You CAN dodge attacks but it's not nearly as reliable.

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I can say I do think the progression of melee weapons (ranged weapon progression seems quite boring and I haven't tested magic recently enough) is quite interesting. A level or two of a weapon skill can completely change the way you fight- which is how it should be!

But I either couldn't get the timing down well (like I said enemy attacks are incredibly sudden) or counter-attacks just aren't very good.

Concerning counters you are right.
I've been digging deep in the engine and as far as i can tell the timings make it very difficult to counter an attack as a result of you noticing the animation. Depending on the move the hit occures at something arround 0.3 to 0.5 sec after the animation begins. As the counter is triggered by a right click and block by holding it down Risen has to wait for you to release the button. That doesn't leave a lot of time to react but you can anticipate when a opponent comes into range and therefore probably attacks.

I doubt that you had more time in gothic 2 but surprisingly the controlls were more responsive.

I always wanted to rewrite the combat AI of Risen and teach it a few tricks for instances charging their attacks to break through blocks but i'm lazy and that's an ambitious project. The problem i have with this is the word "can". Some skill levels are game changing and some are... lets just say i had to read the files defining your moves to find/understand their effect. Ingame they are barely noticeable even if you know what you're looking for.

I could simply be wrong but I'm pretty sure that's Risen 2. Yes, I have to admit a lot are poorly explained.

It took me a while to figure out why I'd use Lateral Blows (slight bonus damage). The explanation when you gain the skill is really misleading. They make it sound like using lateral blows makes you bypass parrying or something.

... and there are far too many counter-attack skills. It's way too hard to counter properly without leaving yourself way open.

On the other hand the Power-Lunge skill (I completely forgot what this was actually called) was probably overall the best skill hands-down.