Marko,
I'll post a more detailed response when I have some time later, but for now:
I've been to Desolation Wilderness twice in the last few years, and both times I did some permutation of the following loop:
Parking lot / bus stop @ Emerald Bay -> Eagle Lake -> Dick's Lake -> over Dick's Pass -> Lake Aloha -> over/down Mosquito Pass and past Clyde Lake into Rockbound Valley via the Rubicon Trail -> through the valley and up the Velma Lakes Trail back towards Velma Lakes and Lake Fontanillis -> back to the parking lot past Eagle Lake.
I think this loop is at least 30 miles, but I'll check and post an actual count. If you wanted to extend it, you could kick around some of the trails to the west of the Rubicon Trail / Rubicon River (e.g. past Lake Doris / Lake Doris / Lake Schmidell). It's kind of difficult to extend it otherwise without going over your mileage limit, based on a quick inspection of the map.
How many miles per day are you hoping to do? There's good camping by virtually all of the lakes, but my favorites are Dick's Lake, Lake Aloha, and Lake Fontanillis (night 1, night 2, and night 3, respectively). That would make for a short/medium day 1, medium/long days 2 and 3, and a short/medium day 4.