Worked for a few years at a (to remain nameless) company that trained corporate jet pilots. We had sims. I am not a pilot, but working there made me very familiar with typical commercial flight procedures and aircraft cockpits. The level of complexity between corporate jets and airliners is pretty much equal. To be honest, the latest and greatest bizjets are more complex than 757's or 767's, including things like heads up displays and moving towards infrared overlays.
Like I said, I'm not a pilot. Zero stick time in real aircraft. But I got to drive a couple of sims--a Learjet and a Citation. I took off and flew the Lear just fine (didn't mess with rudder pedals, just the yoke and the trim switches on it). The Citation was even easier to take off and fly--and with the instructor's assistance, I acquired the glideslope and localizer (radio beacons to assist landing) and landed the Citation. Not well enough to be a great pilot, but not a crash.
Jet passenger aircraft are not hard to fly. High altitude flight can be tougher (thin air, high speeds) but flying around at WTC level is not hard, as long as you maintain airspeed and have the airplane basically trimmed.
Flying jets as a qualified pilot--instrument rated, performing safely and up to standards--that is tougher. That's what flight schools are for. To fly well enough to hit very large buildings is simple.
What the sims and PC sims would have been good for, other than Practice, Practice, Practice would be familiarity with navigational settings. The world looks a little different from way up high. Probably, what they would want to do would be to select a navigational aid (e.g. a VOR) that would get them close enough for visual. How hard is that? Not very. You tune a nav radio to the frequency, you set your flight director (a pretty basic instrument that these guys would be familiar with from sims) to select that radio and some target altitude. The flight director "points" the pilot at both with little v-bars. With a little extra work, they could dial both in to the autopilot and let it take them there until they had a visual.
My long and rambling point is this: the transponder is relatively unimportant in the WTC story and the press and many people are very much overstating the difficulty in flying jet aircraft, especially if you don't intend to land.
sure, it's all fun and games--until someone puts an eye out