Just do it. I had a 2009 Crossplane R1 that was upgraded with Ohlins FGRT808 forks, TTX Mk2 shock, Bazzaz Z-Fi TC, etc., and it still wasn't anywhere near a base 1199, performance-wise.
Like slnvail, I bought a leftover 2012 base (non-ABS) in April 2013. I paid $16,300 for it, and Ducati USA was running a promotion with cheap financing and 6 months of payments pre-paid. I took advantage of that so got my 1199 for about what a new ZX-10R cost.
As was also mentioned, the only issue with the base models seems to be the Marzocchi fork cartridges going bad. Supposedly there has been a fix and replacement parts are different than what came in the 12's. The other difference with 12's is no oil sight glass hole in the fairing. I'll repeat it again, make sure that a 2012 model you're considering has all the updates completed (easily looked up by any Ducati dealer via the VIN). Warranty is strongly recommended.
Which model you choose after that depends on what you want out of your bike. I could have bought an S but wanted to build the bike to my specs and frankly didn't like the idea of first-gen electronic Ohlins suspension. I replaced my fork cartridges with Italian Bitubo gas cartridges and a matching Bitubo race shock. I also got Rotobox RBX2 carbon fiber wheels, the lightest wheels made by a good margin. Between those two upgrades and what I bought the bike for, I still spent less than buying an S model, but IMHO have much better kit.
Since you said you don't plan on tracking the bike, IMHO I would steer you towards the leftover 2012, offer them $15,500 (or $16,000 if it has ABS) and see if Ducati has any factory promotions. Stay with the OEM Marzocchi forks as they are quite good (but inspect them often in case you got a bad set that needs to be replaced with the new cartridges under warranty) and get an Ohlins TTX Mk2 shock for around $1,100. If you like exhausts noise - and with the Superquadro V-Twin how could you not - one of our moderators has a stock-exhuast mod service that makes the bike sound utterly glorious.
I'm not going to lie and say the bike has been as trouble-free as my R1 (remember the cam-chain tension PITA?) or even my MV Agusta F4 1000R was, but everything was covered by warranty and recalls, and it never has left me stranded. Coming up on 7,500 miles and it seriously is the best sportbike I've ever owned after 24 years and almost as many bikes.