Now, here's some actual areas of classic RPGs where I'd like to see some degree of innovation... or simply a return of old features that existed in 20 to 30 year old games but have been long forgotten.
Non-binary outcomes for any major gameplay actions, be it quests, dialogues, or combat. Usually we only get two possible results for any given action: success or failure. There are no in-betweens. The only area where some RPGs give you degrees of success and failure is quests. Kill the terrorists but fail to rescue the hostages, you get a reward but it's not as good as if you managed to rescue the hostages. It's a success, but only partial - you could have done better.
We rarely, if ever, see this outside of quest resolutions though. What about the dialogue checks themselves? If you pick the persuasion option, you either succeed or fail. There is no "You barely persuaded him, but he's still suspicious of you" or "You didn't convince him but you managed to sow a seed of doubt in his mind". Either you entirely succeed, or you entirely fail.
What about dialogue checks that have degrees of success? 1-5 is fail, 6-10 is fail but with a bright side to it, 11-15 is success but with a caveat, 16-20 is success. A major problem of skill checks is that they're binary. By adding degrees of success to them, we instantly make them more interesting.
The same applies to combat. The outcome of combat encounters is binary: either you die, or the enemy dies. Very few RPGs implement a morale mechanic where frightened enemies flee from you. And I am not aware of any that give you full-fledged alternate outcomes that aren't the complete destruction of either side. What about surrendering, both of you and of your enemy? A group of bandits ambushing you only wants your stuff. You can surrender to them in exchange for all the gold in your pockets. Or they will surrender to you if you beat them up hard enough, instead of fighting to the death. They're just in this job to make money, after all. If they're bested by their prey, they won't fight to the death but run away or surrender if there is no other option. This would also allow for dialogue skills to play a role outside of scripted persuasion scenes in quests: if you have a high intimidation skill, you can get enemies to surrender more easily. If you have a high persuasion or bluff skill, you can get convince bandits to leave you some of your shit instead of taking all of it after you surrendered.
Or even just the ability to initiate dialogue during a fight. That shouldn't be so hard. Just add a "talk to" button in the interface and allow it to be used in combat. You can add some cool stuff like being able to talk down the end boss in the middle of combat, rather than having the strictly binary option of "persuade him before combat starts/fight him till the bitter end".
Speaking of combat, it can be made much more interesting by introducing elements like morale and terrain manipulation. Warbanners is a great wargame with RPG elements where every unit has morale that can drop and cause them to flee if too many of their companions are slain or they take a lot of damage. Some units can fell trees, damaging enemy units they fall on and creating an obstacle on the battlefield. Fireballs can leave flames on a hex, which causes damage to a unit each turn it stands on that hex. Why isn't this kind of shit more common in RPGs? It adds so much tactical flexibility, and it enhances the core RPG gameplay of building a party with diverse skills. Having an axe-wielding barbarian in your party who can fell trees in one stroke to create obstacles on the battlefield would be so awesome.
Generally, there's just so much that can be done with combat. A lot of it was already done in pen and paper systems - even in the comparatively simplistic D&D. Just look at Knights of the Chalice 2. Its campaign is unbalanced as fuck, but its systems are perfect. It uses D&D 3.5 rules which have been featured in several CRPGs, but never have they been implemented as completely as in KotC2. And the mere fact that this game implements the ruleset so completely already makes it innovative, and its combat system is one of the best ever seen in a CRPG. It has fully functional grappling mechanics, trip attacks, pushing and pulling enemies, height levels, liquid surfaces, etc etc. You can shove an enemy into a pit and he takes falling damage! You can swim through a lake but suffer reduced movement and maluses to attack as long as you're in the water! You can make an enemy trip and fall, and get attacks of opportunity when he tries getting back up! You can attempt to grapple a dragon with your bare fucking hands!!
Merely going the extra mile to do the pen and paper rulesets you're inspired by proper justice is already innovative, considering how stripped down CRPG combat rules usually are compared to their P&P counterparts.
You don't even have to do anything fancy. Just add basic things like terrain bonuses (height bonus, cover mechanics, etc), flanking and backstabbing, etc.
Innovating isn't rocket science. Just take what's already there and think it towards the next step. Evolve.