Just back from a week-long tour of the ruins in the Yucatan peninsula.
If I had to choose between Chichen-Itza and Uxmal it would be Uxmal.
You will be surprised at how small the site at Chichen is. It's all easy walking. I'd skip the cenote. It's just water.
Three hours is plenty. When you come into the visitors' pavillion, turn right just after the ticket-sellers and there are free maps to be had.
Do NOT forget to take water with you or buy it in one of the restaurants in the visitors' center. If it's a hot day, shade is in short supply.
Taxis at Progreso are flat-feed, no negotiating. So don't even think about it. If I remember, it's about $60 US each way. You can do better by renting a car if shaving a few pesos is important to you. Roads are VERY well-marked.
No reason you can't climb the big pyramid. Your wife can stay on solid ground. I'm like your wife ... I don't climb. Actually, I can climb, it's the coming down part that flips me out.
I should have a bunch of pix up on my personal website in the next day or two. <http://happysails.com>
Let me know if I can help more.
pamda -- CM First-Time Cruisers Editor and Ruin Maven
p.s. You might want to check this out ...