As a current owner of several KTM V-twins I absolutely love the brand and I can certainly see your atteaction to the 1290 SA. The 1290 and the Super Tenere were both fighting for first place on my short list. Earlier this year, a lightly used '14 ST won the fight and is now in my garage next to the WR250R and Katooms. Seven months and 8,000 miles later I couldn't be happier and I probably saved about $11,000. The Super Tenere does everything that I ask it to do and then some. Based on the absolute ton of research that I have done over the past several years, the Super Tenere is the bike that I would take to the ends of the earth and back with total confidence (as long a there isn't deep sand involved.) I really like the extensive dealer network of the Yamaha brand, however, it is comforting to know that I'll most likely not have to visit one, unless it is for some scheduled maintenance that I don't want to attempt (valve check/adjust, maybe.)
Though I bleed orange out of one arm and now blue out of the other, my advice to you is to just keep your Super Tenere and do the mods that tomatocity recommends. BUT, if you must have the extra power, cruise control, suspension, etc, then by all means buy the 1290. Just plan on keeping for quite a while because, like most European bikes, you'll lose your ass with depreciation. (Ask me how I know) If you are buying new the $4,000.00 discount that you are referring to will certainly help to a degree, but as soon as KTM offers something bigger and questionably better the depreciation will further increase.