I'm always surprised when people suggest dropping Munich from a trip to Germany. That may be because Munich is a lot like many American big cities, plus it's in flat land and spread out. Most tourists only see the small old city center, maybe the museum district, and, in season, the festival grounds. That's too bad, because Munich is a great city.
But you're asking about Nuremberg, and the surrounding "day trips". Well, lets start with those. Rothenberg is, in my mind, best first thing in the morning. It's okay at night (but nowhere near as good as Prague after the sun goes down), but on a sunny morning when the mustard is in bloom it's fantastic. Tourists don't usually arrive before 10am, and that gives you time to get a fresh pastry and coffee, walk the walls almost alone, and get your pictures before you have to fight the crowds.
If you want something unique, consider staying at Castle Colmberg instead of in the city. It's about a 15 minute taxi ride from the Rothenberg Train Station.
Bamberg is nice, and the walk along the river is very picturesque. And Wurzburg is also a good city to spend some time in, especially if you like wine and are visiting in the fall. But frankly from Nuremberg the place to go is Regensburg, because you can actually walk the old town in a day, and it's quite pleasant. Wurzburg is too big for a "day", especially if you try to hit a vineyard or two. And Bamberg isn't as nice as Regensburg (in my opinion). If you want someplace not on all the tourist stops, consider Amberg (east of Nuremberg), or Ansbach (to the Southwest) both of which are very pretty small towns well worth visiting.
There's just so much to do in and around Nuremberg that it's hard to know where to start. For hotels I like Le Meridian. The Victoria is good also. I've also used the Ringhotel Loew's Merkur, which is on the other side of the Bahnhof. If you want American amenities the Sheraton is just a block away.
My basic list of things to do in Nuremberg is as follows:
The Train Museum
The Toy Museum
The Kunst Quarter
Westfriedhof - Cemetary
Johannis Friedhof – Tomb of Albrect Durer
The Cupernicus Planetarium
Kristall Palm Beach (not really in your focus, but a lot of fun...)
The Water Gate
Imperial Castle & Gardens
National Germanic Museum
Beautiful Fountain (Schonnebrunnen)
St. Giles Church Frauenkirche
Albert Durer House
City Museum (Fembo House)
Tiergarten Tor - Medieval Square Frauntorturn District - half timbered houses
Zum Guldenen Stern
St Sebaldus Kirche
You might also want to check the calendar for the Messecentrum and see if they have a show going on while you are planning on being there. First, because that affects hotel availability and pricing, and second in case it's something you're interested in.
If you only have two days you'll have to pick and choose. Note this does not include any of the WWII places, which could easy make another list.
The popular walks in the evening are those along the Pegnitz river, which flows east to west thru the old city. The other is the red light district, which is along the old wall moat between farberstrasse and the Spittaltor (tower gate) in the south west corner of the city wall.