I've had my 04 Gemini 2000 for about 6 weeks. I'm 6' and 225 lbs. Bought it as a do-everything aggressive trail, freeride and downhill bike, but kept my hardtail for xc. I've put the bike through its paces and am very pleased so far. Very light, pedals great and the suspension (once tuned properly) lets you role over just about anything. It is also a great value.
Re Stem - I have to agree with you about the rather spindly stem. Certainly not consistent with the bike's capabilities and although it is still intact and does its job, it doesn't inspire confidence. That said, it is easy to swap out for a beefier stem from Raceface, FSA or Woodman Components which I'll probably do in the near future.
Re Rims - Initially, I was a bit worried about the strength of the XM321 rims. They're supposed to be Mavic's cross mountain rims but are actually the same as last year's F219 which came stock on my son's 03 Stinky. His wheels are still in good shape after almost 2 seasons of harsh dirtjumping, freeriding (including drops to flat) and downhilling. As for my wheels, the are still perfectly true despite some rough runs through rock gardens with basketball sized boulders as well as my "less than smooth" style. I haven't even had to tighten the spokes yet. Cannondale apparently handbuilds the wheels which seems to contribute to their quality. When they wear out, I'll likely buy something better but they're good for now.
Re Tires - My Gemini came standard with 2.35 Maxxis High Rollers (Super Tacky). Despite being 2.35, they are pretty small (about the same size as the 2.1 Velociraptors on my xc bike) and I wasn't getting the grip on dirt that I needed from the smallish knobs. I also discovered that they are the single ply version so the sidewalls are quite flimsy. I've since put a 2.5 Kenda Nevegal on the front and a 2.35 on the back (both with downhill casing). The difference is amazing . . . my Gemini now feels much more planted and inspires even more confidence. Weight is up about 2 lbs and I've given up some pedalling efficiency but worthwhile in my opinion. Highly recommended . . .
Overall, I have to say I'm pretty pleased with the Gemini. It has certainly taken my riding up several notches and I'm nowhere near riding the bike to its potential.
Hope this helps you with your decision. If you'd like to know anything else, post up and I'll get back to you.