I'm going to go along with Tristan on this one...
I became an avid MSFS user long before setting foot in a real light airplane, and I feel that it really helped me. It didn't help at all with the actual manipulation of the controls and getting a feel for the plane, but what it did help me with was the "book" knowledge, procedural knowledge, and above all else, radio work. I'd say use MSFS (I have the 2004 version, and it works just great for me) and go through the "Lessons" for the Private certificate. You have to suffer through Rod Machado's "humor", but the material is presented in an easy-to-understand manner and it applies to real-world flying.
Also, the in-game ATC is pretty accurate and helped me to learn the lingo, though I did have to break one bad habit from that - using the phrase, "With You". NEVER use that phrase in real life, and if you do, for your own safety, don't admit to it on this board or else you will spark off a huge fecal-material storm. After getting used to the in-game ATC, I would sign up for VATSIM (
www.vatsim.net). This is a free online network of MFS pilots and ATC's that use voice chat through your computer headset. I think this above all else helped me with my radio work. Back when I was a nine-hour student, I flew around the Houston Class B with the guy who would later become my mentor in his Bonanza and he thought I was a high-time licensed pilot simply because of my radio work while talking to Approach. It's always been one of my strongest points, and I attribute 95% of it to using VATSIM on MSFS.
I also agree with the above point of "preflying" your x-c trips in the sim. It will help you get a gauge for time between waypoints, and most things on the sectional charts are pretty accurately depicted in the sim (at least the charts that were current in 2004). Also, most ATC frequencies you switch to in the sim are going to be the same ones you'll use in real life, so when you get a handoff from ATC, actually tune the radio yourself instead of just hitting '1' to have the game do it for you.
So, I say use MSFS, but start by going through the lessons. I wouldn't even waste money on a yoke, just get a $30 joystick... the yoke won't help you learn how to drive the real airplane anyway. If you do it this way, then the only bad habits I would think that you'd have to break would be looking inside the cockpit too much and using that bloody "With You" phrase on the radio.
Disclaimer: I'm not a CFI, so consult with yours before you proceed with my advice. I'm just speaking from my experience of going through my student pilot training and becoming a Private Pilot.