ctk333, rockers are "rocker arms", like traditional rocker arms except there are two rockers per valve: one opening rocker and one closing rocker. Instead of the valve using a spring to close it, the two rocker arms are actuated directly from the camshaft, which in-turn has one lobe controlling the opener and one lobe controlling the closer. The tolerances are very precise and there is no valve float, even though spring technology has progressed since the desmodromic valves were introduced, thus making the 'no valve float' advantage moot.
Where the rocker arms contact the cam lobe surface is where the flaking happens. The rocker arm contact face is hard chromed, and the hard chrome surface eventually degrades and flakes, ruining the rocker, possibly the camshaft and even possibly damaging the engine internals. There are a few fixes for this, but none are free, and can range from $50-$79 per rocker arm depending on what you get. Remember, there are 16 rocker arms, so $$$$$$$$$$. Ducati *may* offer a "goodwill" warranty on the rocker arms, but only for parts; you pay the labor.
Generally, IMO, the newer the bike the better, as long as the engine/bike has documentation. Just like any vehicle platform, evolutionary changes happen over time, so the niggling problems on early bikes supposedly get fixed with each new iteration of the design. The 998 is probably the most reliable, if only because the testastretta engine isn't prone to some of the desmoquattro issues, and you'll find more low mileage 998's than anything else.
Just for reference, my 2000 996 was average I guess, and made 113hp/68 ft.lbs. at the rear wheel before the engine blew up. I'll also align myself with those that say the upkeep of a Ducati will be more, because it's been that way for me. Even little stuff like bolts vibrating loose has really bugged me. At my last track day, I lost a few bolts due to vibration: three holding the front "V" cowl (both lost at once, a replacement one lost a session later!), seat lock cylinder vibrated loose and carbon exhaust guard bolt worked its way loose. My engine blew up at 12000 miles and I was stupid enough to rebuild it. It's terribly uncomfortable, gets pretty crappy gas mileage since the engine rebuild and finding parts can be hard at times.
I love it though, and can't imagine owning any other sportbike.