I stayed at Hotel Edelweiss in Mürren, and would do so again (found in Rick's book). For all Swiss hotels, I found better prices and room availability by e-mailing them directly, compared with booking on the websites. Be sure to say you found them in Rick's book for better prices!
If the Schilthorn is your primary interest, staying in Mürren is better, because coming from Wengen will entail more travel time. By the time you get from Wengen up the Schilthorn, there's more chance the weather will have changed. Of course, visibility can change in minutes, as you'll see once you're there. If you have iffy visibility, a great thing to do is the Allmendhubel. The view is not as good as from the Schilthornbahn, but cost is much lower as well.
Conversely, if going up the Jungfraujoch is your priority, staying in Wengen shortens your time to get up there. And staying in Lauterbrunnen splits the difference, at the cost of views (in Mürren I had amazing an view right from my room, which was practically hanging off a cliff!). I also didn't like the town of Lauterbrunnen as much as Mürren; I didn't look around Wengen, but it's larger than the others.
As for ease of transportation, all the towns are connected (details are in Rick's book, and will be much clearer once you get there). Some seem to mind schlepping their luggage up to Wengen or Mürren, but you only have to do that on arrival and departure, so for me it was a non-issue. I did like that from Mürren, you had easy access to both the train and funicular to Lauterbrunnen (with further trains to Interlaken or Wengen/Jungfraujoch) and to the cable car to Gimmelwald/Staubach (going down) or Birg/Schilthorn (going up). The train and cable car are at opposite ends of town - which means a 10 minute, largely level walk.
As for restaurants, I had good food at several of the restaurants in Mürren (many are in hotels). My one meal in Gimmelwald, at the Pension Gimmelwald, was of notably more "basic" quality (think fuel, not cuisine, as opposed to Mürren restaurants, which featured cuisine).