That's exactly what I'm dealing with and feeling. The action seems fine on mine, nut and saddle look good, setup looks great overall...so it's hard to figure.
I have the same problem with easy chords being unusually difficult to get to ring clearly. Stiff as a board in the neck...to me it feels like the neck.
It's an illusion. It's more likely the neck profile itself.
In any case an actually stiffer neck would be a good thing for overall life expentancy of the instrument. What they really do is build 3-pc necks with a centerstrip when they want to increase torsional rigidity of the neck. That's more of an anti-twist than anti-bowing measure, though.
When I got my D40 I thought it had a different set-up than the D25 because it felt like my first 1980's Fender MIK acoustic ("Set up in the USA" on the box) and I thought "Ah, built in Corona, it's got the "Fender set-up" on it.
So out came the ruler and lo and behold it's virtually identical in all set-up specs to the D25 and they both had the same factory L350 lights on 'em. It was a puzzle to me.
Only a while later did I realize one night that the D40's neck was significantly deeper/"chunkier" than the '25's and then the light went on.
A few years later as my grip changed I realized it's actually easier than the D25 now for scales up above the 5th fret.
I wonder if adding a little more relief would help it.
Actually you'd want to
take out relief (flatten it).
But even that will only gain you a miniscule amount of comfort.
Thee 2 biggest factors here are action height and string tension.
Going to .11's should help and I'm not sure about that metric spec but in fact don't be at all afraid to go down to 5/64 on the bass E (if that's a bit lower than 2.5mm) and 4 on the treble.
And double check the clearance at the nut. That's usually the primary source of the perception of excess stiffness because the closer to the nut you fret, the shorter the lever of string length becomes when fretting, so more force is required to get clean fret contact.
One last desperate measure:
Tune it down a whole step instead of a half step and it'll be easier to play with the GF?
On another member's suggestion, I did this to my F65ce only a couple of weeks ago, expecting to be a bit disappointed but trying to keep an open mind, and I was completely surprised at the transformation, like that guitar was actually choked off for its whole life and was finally able to really breathe!
What've ya got to lose?