My parents just returned from a guided-tour vacation with CIE and had a wonderful experience. I cannot speak to the "go-as-you-please" vacation specifically, but if it is anything like the other, you will be in very good hands. They provides every bit the experience that they claimed and were most helpful to my parents throughout the trip. As a matter of fact, my fathers luggage was misplaced by the airline (flew Aer Lingus direct flight from Chicago) but CIE dealt with the airline and made sure that the luggage was sent to meet their tour. That was the one and only negative from their trip - and it had nothing to do with CIE! So, with that said, my guess is that you would have a very good experience with them.
On a side note, I am going to Ireland in two weeks with a friend and we contemplated the very package you are interested in but we decided to just go-it-alone. We just decided that this was going to be the best option for what we wanted to do.
Both are reputable companies. Whether you choose a go-as-you-please vacation will probably be determined by cost (remember if there are two of you going you must multiply the cost by 2) and time of year. It is easier to use vouchers in the off-season. Keep in mind that not all places take the vouchers so that will limit you. If you are going to Dublin you will need to upgrade to hotel vouchers as I can count on one hand how many B&Bs in the Dublin area take them. You can do a search on the forum for the subject of vouchers. We have had many long discussions about the pros and cons of the system.
Do the math for the go-as-you-please vacation and doing it on your own. It will most likely determine which way to go.
My last trip was a GAYP with CIE Tours and we were very pleased. I'm still using the guide books and maps that were part of the package. They scheduled a castle hotel stay and the medieval banquet at Bunratty along with reserving our vehicle (had a problem with Hertz but not CIE's fault. Never occurred to me to contact CIE at the time) and providing en suite vouchers for the B&B stays. Only one place charged a supplement.
All that said, we are going to do the next trip ourselves, with a great deal of help from Michele and her leprechauns on this forum.
We did our car rental through 1-2 Travel, as they offered the best price. No problems whatsoever, and they provided good customer service.
Haven't used them for anything else, though. I'm leery of vouchers, as I've heard that the B&B operators aren't always fairly compensated for them. I've also heard that if you're up against a customer paying the regular rate for a room, the person paying full fare will get the room instead.
You are right that vouchers can be a problem. It depends on when you use them. Off-season is best. It does limit where you can stay and the B&B owners do not get full value for their rooms. The travel agents and others take a piece of the pie, leaving the owners with a greatly reduced price. However, in off-season when they would not be full it provides extra income that they like then. There have been many discussions on the voucher topic here. If you do a search on the forum you will probably find a million.