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The biggest single difference is the fact that down the line, should you want to, wooden doors can be sanded and re-finished. This has the potential to significantly extend the lifespan of your investment. It is possible to paint MFC and there are specialist products out there to allow you to do this but in my experience the finish will always be somewhat fragile and much more prone to chipping.
Aside from that it's worth being aware that there is an enormous gulf between good MFC and cheap MFC.
The cheapest way to make MFC or MDF doors is to cut the profile on a CNC machine and then apply a heat shrink foil. This will always look good in the showroom but living with it presents...... Issues as heat (for example if the door lives near a stove) will cause the foil to shrink back further and produce puckering at the corners (I've attached some photos as an example). The best MFC doors will either be constructed in the same way as solid wood doors by forming rails, styles and panels or will be solid panels (something that you can't really do with solid wood due to cupping and dimensional change). Either way when you spec this all of the components are cut from a large sheet of MFC then have a high quality edging applied which makes the panels pretty much water proof.
Dredging the kitchen chat... currently have a quote from a big kitchen place and an independent chap.
Does anyone have any real world experience of MFC doors vs solid wood? It's the only difference between the two quotes, with each party recommending their choice as the best...