I encourage the idea of a used Dave Smith Prophet '08, a 61-note instrument. Prophets tend to come with a generous number of useful presets straight from the box. You get enough knobs that you can easily learn the major moves you'll want to make most often. Tweaking the filter for a brighter sound or adding a little time to an envelope's decay and release for a longer fade-out will become second nature. I politely advise against the Roland JD-Xa, as its a hybrid synth that calls for a little more programming experience to apply readily. The new Yamaha MODX is retailing at $1299, to great reviews. Its heart is a touchscreen that's easy to use and it sports just enough of the right knobs and sliders, IMO. As a serious organist with some SK use under your belt, I suspect you'll make the connection between playing drawbars and playing knobs more readily than you might think right now. Don't buy a used instrument that's too close to "vintage," as they often have expensive repair issues due to age, just like us.
I don't think you really want a totally analog instrument as much as a ROMpler (Read Only Memory), which offers samples of both acoustic and electronic sounds. While there is always a lively debate about the nature and quality of sound-production methods, ROMplers often come with a few permanently assigned knobs and then some which are user-assignable. The MODX could add choirs, bells and the like to your organ palette, while those knobs would teach you the basics of synthesis. Its win-win for newbies. Whatever you buy, don't be too daunted, because we all embrace the complexities until we find the right personal zone. The goal isn't necessarily to become a technical expert, but to expand your own musical range. I envy you a bit, because you're about to have the great rush of fun that comes from the newness of it. I wish you good luck as you proceed.