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Ok.  Mucked around with Permanent Skills for a bit.

I moved all my equipment to my inventory storage and experimented with playing with just the Permanent Skills at level 50.  They weren't as potent as the gear is, and the Rogue-Mage build is definitely fragile without all the HP, Armour, and Resist the gear provides.  Still, higher level threats are going to be necessary to really see how it all comes together.  At this point, even at level 4, there's nothing really challenging my build.

I like the direction the overall Skills go, particularly for Rogue and Mage.  Warrior feels like it's too focused on dealing Damage, and might be more appropriate as focusing more-so on survival.  For example, Bleed and Poison are kind of redundant at this point, so leaving Poison in Rogue and replacing Bleed from Warrior with something like a chance to attack and destroy incoming enemy projectiles with an Auto-Attack might be cool.  Similarly for the various other overlaps, like basic Attack Speed passives.

The XP Boost in Rogue also doesn't really amount to much.  Even at Rank 5, it only got me 1 extra level-up on the Level 4 map.  This is common in a lot of games that offer XP Boost.  Unless you're offering something like +50% at Rank 1 up to +250% at Rank 5, players are unlikely to see much of an impact with the increasing XP costs of level progression.
An easy way to project the impact is to write up a chart of the XP needed for each level, and then at the XP Boost percentage in another column, then compare what level that would actually wind up bringing the player to.
For example, from Heroes of Might and Magic, a popular turn-based strategy series:



Ultimately the Learning Skill, even at +20%, only amounts to one extra level for the player for the Levels 10 through to 24 range.  Outside of that, the Learning Skill's Experience Boost is entirely pointless and a considerable waste of Skill Points.
As such, in later sequels of the game, the Experience Boosting Skill was also bundled into something else, such as bonus Characteristic Points per level.
Something to consider for NXF.