I don't own an 89F, but I do own a 59 and a 69S, and they do play and sound different -- the mags for sure, but even the models are influenced by the physical configuration differences to some extent.
The tone woods, whether the guitar has a mahogany body & set mahogany neck (59) or an alder body and bolt-on maple neck & rosewood finger board (69) makes the physics of the units different -- and those do influence the vibrations that the piezo's pick up and the electronics shape for the modeling. I love them both for what they are. I did switch out the 69S's 3 single coil pups for noise cancelling units, as I had gotten spoiled by the lack of noise of hum buckers even after many many years of being a Fender guy...
I find myself using the mag PU's probably 80 - 90% of the time, and the models for certain signature sounds, plus of course the acoustics and specialty instruments, like the banjo.
On the models, I find the 59 nails the hum bucker guitars a little better than the 69, but the 69 nails the Fender-centric models a touch better. Both are good at all the models, but they tend to edge out the other for models more in their physical realm. Part of it could well be the feel and visual vibe, too - I admit. We are influenced by what our eyes and hands tell us as well as our ears, but that's my take on it.
If you can afford to keep your 59 and get the 89F, I'd suggest it. I personally was not as attracted to the 89's aesthetics, nor the 89F's FR whammy as I was initially drawn to the 59, and then the 69S when they came out with the classic 3 single coil PU's, which is when I jumped for the 2nd time last fall. But those are personal preferences only -- that's why it's nice to have the choices between the different models of the JTV's.
Line 6 could expand those as well to semi-hollow and other body styles to attract players in those areas. The 3 basic styles they have now cover a LOT of players' familiar territory. One big thing L6 should work on is a left-handed version of at least one of the JTV body styles -- I think they have lost that segment of their target audience. Potential LH customers were begging for the LH models a couple of years ago, but you don't hear it so much, lately... Too bad...
My 2 cent's worth -- I'm sure you will get many other opinions on the subject. Now back to your regularly scheduled question...
Line 6 Gear - Variax 300; JTV-59, JTV-69S, Pocket-POD, POD XTL - (RIP), POD X3L, HD500, HD500X, HELIX
1966 Gretsch Country Gent, 1973 Fender Tele Deluxe, 1978 Strat, Epiphone LP Classic, Epiphone Special with P-90's
Gigging Amps: Quilter Tone Block 200, Crown XL1000; Yorkville NX35 Speakers