[Army Guy]

NJ BLue, first, you will an EXCELLENT time. I lived, ok I was stationed in Europe twice for a total of 4 years, so I can definitely help you as I have done all three of your options. But the first question I must ask is how long are you going for? That will really determine what you need to do.
Option 1: Bus tours are ok, but only if really pressed for time and want to see the most in a little period. But as you said NO flex at all. Yes, they will tote your bags, but my suggestion is pack light. And I suggest this for all the options. Pick things you can make many outfits out of, and remember Europeans unless you are young, dress more formal then we do here. What I mean is you should pack like chinos, dress slacks and golf type shirts and a windbreaker or sport jacket ( Europe is a higher lat so not as warm as here even in summer.)
Option 2: Car Rental is higher in Europe and so is gas. BUT you have control of your time. The signs are very easy to understand as they use graphics like we do here. Just the City Names are spelled out and Ausfahrt means "Exit". I knew a guy whole kept asking just how big this city of Ausfahrt was! But to REALLY see Europe this is the best way. Parking in Cities can be a bear, so park outside and use mass transit in.
Option 3: Trains and mass transit in Europe IS WONDERFULL!!!! Nothing like the US, they go to just about everyplace you want, and you can get a Railpass cheap, opt for 1st or Erste class, it is well worth the cost which usually is not much more. It is less crowded and you can make reservations for actual seats within a compartment.
Needless to say I could tell you volumes more, PM or email me and I will give you more details.
But your choice should be based on time and what exactly you want to see cover, Europe is FULL of stuff, and I could easily spend 1-2 weeks in just one of the countries you mentioned.

Army Guy