I just got back yesterday from Ecuador using a tour company (GAdventures/National Geographic). I went to all of the places you listed with the tour group and on my own. You don't mention how you're getting around. If you drive, be aware it's crazy-pants driving - horn and accelerator in equal measure. Quito traffic is a nightmare. Sunscreen is mandatory - even if it is cloudy, the elevation makes the sun much stronger, even if it isn't hot. The weather forecasts are always wrong. Also, they have the most amazing fresh fruit - eat as much as you can, you won't have it any better. Here's my two cents on things to do:
Quito is high elevation (9000 feet). I knew that, but it was a surprise how winded I got just walking around and I had an altitude headache for several days. Give yourself time and drink lots of water. Old town is a bit sketchy at night, keep your wits about you. I did a middle of the world day tour with CarpeDM. Private car, and they take you to the real equator (not the tourist monument) and the Intinan Museum which was fun. I enjoyed the Casa del Alabado museum. It was the end of the wet season, and it rained every day. If the thunder starts and the locals start running, RUN FOR COVER. I enjoyed a nice meal at Casa Warmi in the new part of town. Also ate at Tianguez, just under San Francisco church (it was just fine).
Otavalo was mostly focused the market. It's overwhelming on the weekends, and personally I liked the smaller markets in other towns we visited. Watch your belongings, one of my tourmates was pickpocketed. Peguche waterfall is a nice hike. Peguche Wasi shop had nice products and demos (we ate there too and it was amazing, but not sure if that is only for tour groups). We stayed at Hacienda Pinsaqui - lovely location, super comfortable beds, decent food (though spendy for Ecuador).
Papallacta we stayed at Termas de Papallacta - fantastic, you have thermal pools right outside your room. They have public baths too (I didn't try them). There is a great loop hike above the hotel - follows a pretty river. We ate at one of the little restaurants near the entrance to the hotel (I don't recall the name). There are a row of them, it was the farthest from the hotel entrance. Had spectacular trout dinner.
Tena our group stayed at a Itamandi EcoLodge which is a bit up from Tena. Didn't actually spend much time in the city proper. If you have a chance to go into the jungle, do it, beautiful. Yes, there are mosquitoes and I got bit several times but mostly where I missed applying bug spray. Wear long sleeves and pants. I've never seen it rain so hard as I did in the jungle. Nothing dries out either, so bring ziplock bags for things you want to protect.
Baños is a cute town. There are nice squares, the church is pretty. Some of my group ziplined and had a blast. I enjoyed a really good dinner at La Closiere de Lilas. The market has cheap eats and great fresh juices. If you go to the public baths, here's the drill: pay entry fee ($2 day time, $3 evening). There are two levels (entrance level is mostly covered, the top level is open air). There are changing rooms. Put your things in one of the plastic crates and take to the counter where they'll give you a wrist band and store your things. Swim caps mandatory (you can buy for 50 cents at the stores around the baths, or rent them at the place). Shower before you get in.
Cotopaxi - surprise, it's at elevation! I believe guides may be mandatory, stop at the park entrance to get one. The mountain was mostly hiding, but still beautiful.
Have a wonderful time. PM me if you want more info.