Yellowstone/Grand Teton
 

We are traveling in September to Yellowstone/Grand Teton. Suggestions please! We have 12 full days to spend in parks. How should we split it up? We are hikers. Also, cabin rentals and suggestions?

Can't help you on lodging as I camp. Can however suggest some great spots to check out.
In the Tetons - along US 191 north from Jackson past the signed Glacier View turnout look for a small sign on the left indicating a raft put-in. This is Schwabachers Landing. Follow the road to the end (past the put-in) follow the trail several hundred yards and will come to several lovely beaver ponds. The dens were active two years ago when I was there. A popular spot for sunrise as can get the peaks reflected in the ponds. Good also for moose. The Oxbow is another good spot for sunrise/set. If you continue about .8m past Oxbow towards Jackson Lake Lodge turnoff will see unmarked dirt road on left. This leads about mile back to the river and another put-in. Good for birds and moose. Both sides of the road from this road to the Jackson Lake Lodge is good for moose. Across the road from the lodge is Christian Pond which ususally has a couple of trumpter swans on it. For hiking would recommend a three day two night loop (can be shorted to half that) Starting at Lupine Meadows near the Jenny Lake ranger station and either walking around the lake or if still operating that late in the season the boat ride across the lake to Hidden Falls. Continue past String Lake and pickup the Paintbrush trail. This will take you to Lake Solitude and on to the jct with the Cascade Canyon trail. Take this back down to Hidden Falls for a shorten hike. I found the second half to be much more intersting as you are walking behind the three main peaks and are above treeline for most of the trip. From the Lake Solitude/Cascade Canyon jct continue on to Alaska Basin (trail) then come down Death Canyon trail to walk past Phelps, Taggart and Bradley Lakes back to Lupine Meadows. When I did this loop in late July the flowers were spectacular A couple of nice day hikes are to Amphitheater Lake or around Jenny and String Lakes.
In Yellowstone might try Heart Lake trail back to a thermal area not often visited. Lamar Valley is the place if want to see wolves. Early and late are best. Just drive the road til find the "wolf jam". A spot that is usually good is near Soda Butte. The trail to Specimen Ridge and petrified trees (hard to find) is also on this road. Mt Washburn (either direction) is nice day trip to the tower with chance to see bighorn sheep. Observation Peak and Grebe Lakes are nice day hikes. Be sure to check the park web site as some of the roads are closed for construction.
A couple of good books are Yellowstone Trails by Mark C. Marschall and Teton Trails by Katy Duffy and Darwin Wile.

You are going there at a great time of the year. The foliage will be great...and so will your experience.
The best advice I can give is to get a copy of Frommer's guide to Yellowstone and the Grand Teton. It's a excellent source of all the information you asked about plus a lot more.
12 days in the Teton and Yellowstone in September? You don't get any closer to paradise!

We stayed at Signal mountain Lodge cabins last summer... very nice, rustic and right on Teton Lake. I'd recommend them. In YNP the places to stay are the usual, but it's worth it to be IN the park, rather than driving in each day from West Yellstn

One place I recommend you avoid is the cabins at Yellowstone Lake. I'm sure some people have had good experiences there, but I haven't heard any of them. :)

Another vote for Signal Mountain!

In Yellowstone we stayed in the center of the "figure 8" road (at Lake Lodge)and saw a quarter of the park at a time. That worked well for us. As someone else has mentioned, all of the accommodations are very basic and some are better than others.