We did Chichen Itza from Cancun a few years ago (company sponsored trip). It was an all day thing (7+ hrs), most of it traveling on a bus. We stopped at a local market on the way to be pestered into buying local wares, and on the way back stopped at a neat little restaurant next to a huge sinkhole/ water filled cave. Some locals would dive into it, and climb back up which was pretty cool. The ruins I thought were very impressive. I had only been to one small ruins in Cozumel, and CI blew it away! Its hard to imagine how they could build stuff like they did without modern machines. The big temple was still open to tour inside (we skipped it since the line was long, but heard you had to crawl through some tight spots and it was very hot and amp) and we did climb to the top of it (looks easy until you start, then you realize the steps arent very close together. Coming down was a bit scary-I sat and crawled down each step since I felt like I was going to fall off)! Im not sure if you can still do these things though. Its worth the trip, but since its so long, you might want to stick with a ships tour if they have one to be sure youre back in time to sail. Id be worried the whole time about missing it!
We have toured several Mayan ruins in Yucatan. The inland ruins are much better than the coastal ruins. Chichen Itza is one of the better sites in the inland. Uxmal is another good site. But its pyramid is not as famous as Chichen Itza. However, it is closer to Progreso. If you decide to go to Chichen Itza, you should seriously consider using ship's tour. There is no advantage for using private tour other than shaving a few dollars. It is a long way and anything could happen, for example, bus failure on the way back. In Mexico, tour guides must study and pass examinations to obtain license. Taxi driver is not allowed guiding tours. If you need more information regarding the Yucatan area, please let me know.