Riding position aside, the two aren't that dissimilar in terms of power, weight, speed, geometry, design configuration and quality, but there are a number of reasons I wanted to go back to an SP, and an SP-2 in particular:
1) I prefer the engine. It probably doesn't feel quite as lively/revvy as the Rotax lump, but it's about 10bhp more powerful, more progressive and feels much more precise. In short, it makes less fuss about doing its job and feels like a classier, more powerful design. Having ridden a few Ducatis (and found the engines similarly rewarding - when they work!), I'm inclined to believe that some of those characteristics I favor are probably a function of the 90 degree design. Not too keen on the KTM 950/990 engines for similar reasons. Whilst we're on the engine, I may be committing heresy here, but the SP sounds better, especially with the gear cam whine.
2) Despite having similarly tall (if not taller) gear ratios, the fueling is much smoother and more predictable from a closed throttle at slow speeds (that does not go for the SP-1), which is especially important in tight, slow speed corners. I'm well used to big twins, and found the Tuono generally very good in terms of fueling, but the somewhat jerky delivery of the Aprilia at low speeds and low throttle openings became pretty irritating. And the shoddy shock on the 1000R didn't help either when trying to take tight bends in an enthusiastic manner.
3) It's much more planted. I found the Tuono skipping all over the place when ridden hard, which was great fun for a while and on the right road, but ultimately I wanted a much more solid front end that provided more feedback when on the throttle.
4) I got very bored with windblast on a recent trip to the 'ring on the Tuono. Admittedly, prolonged stints at 140 on the Autobahn didn't help, but I envied others on faired bikes at the time. On that note, given the fairing, I find the SP is a fair bit stronger at the top end of it's speed range, reaching 165 with relative ease. That's obviously not something we often (if ever) need, but it's true nevertheless. Whilst we're on the fairing, there's loads of space in the SP-2 tail cowl for bits and pieces, and barely any in the Tuono. Small things, but details matter..
5) The SP's a more challenging ride and demands more attention, but it's ultimately a more rewarding one and after doing over 10,000 miles in a year on the SP-1 (before I had the Tuono), I never felt indifferent about heading out for a ride. It always had a sense of occasion. Unfortunately, I can't say quite the same for the T after 6000 miles. It was a little too easy to ride fast, but frustrating when I wanted to ride faster.
6) The Tuono's a looker, but I've always thought the SP-1/2 is one of the prettiest bikes and most elegant designs to come out of Japan. The HRC build quality and heritage also appeal. I think the Tuono is actually a much better made and engineered bike than a lot of the stuff coming out of Japan of recent years, but the SP-2 is an exception, and from an engineering perspective, a lovely thing to behold.
7) I may be completely wrong, but given it's rarity - and assuming I take care of it and don't put tens of thousands of miles on it - the SP-2 is unlikely to depreciate much (if at all), making it a considerably better investment.
At the same time, there are a number of sacrifices made in changing from the Tuono to the SP: The Tuono is comfier (both in terms of riding position and ride - the SP is extremely firm (might as well be a church pew). It's also more practical, more fun on bumpy roads, has slightly better feel and strength from the front brakes, is a little lighter, has better pillion provision, makes a better tourer, has longer service intervals, is probably a little easier on consumables and cheaper on insurance.
It's also worth noting that almost all the niggles I had with the Tuono are probably addressed by the Factory suspension and sprocket changes/custom fuel mapping, but I haven't tried a properly sorted T so I couldn't say for sure.