My little grain of salt...
I did too change the big daneaxe-like axes in my game via Morgh's tools (one "war axe", one "2h axe" and, of course, "my wife") to polearms. Their length is, even if a bit shorter than regular polearms, quite similar to the (much later) pollaxe, which cannot be wielded like a regular "2 handed" weapon. I recently acquired a replica of a dane axe, and you definitely cannot use it which two hands at the bottom of the shaft. Both grip and techniques are much more similar to polearms than two-handed.
As for changing only animations, it does work, but only in one way: you can have a 2h weapon attacking like a polearm, but it will still be gripped (when not attacking) with two hands at the bottom. A shame, really, for you'd want shorter 2h axes to be gripped like polearms, and attack with devastating 2h animations. I did settle with changing only the parry animations to polearms for them, and I am quite happy with the result.
So I did test: real dane axes as full-fledged polearms, and other big 2handed axes as 2h, but with polearm parry animations. I am currently to day 400-ish and quite happy with the result.