The Paris Museum Pass is the one you need, if you want to avoid waiting in admission lines. Look for the signs indicating "ticket holders or Pass holders" and enter there. But everyone must pass through Security, no matter where you go. The PMP does include most of the museums and major attractions, and you can re-enter on the same day. You can purchase this in any tourist kiosk in the airports or major train stations, or simply buy it at the first museum or attraction that's covered in the PMP.
But you should compare prices and be realistic about how many museums and attractions you think you'll really be able to manage. Individual prices might end up costing you far less, and if you time your visits to arrive when things open, or later in the evening, you'll find that lines will be much shorter.
As far as transportation goes, Paris is a small city and very walkable, so you might have more fun just wandering from one attraction to the next.
For only 3 days, you could go with either "carnets of 10 loose "t" tickets" that anyone may use for a one-way trip on Bus or Metro/RER - each "carnet" costs 14.10 EU, and you can buy single tickets if you run out.
If you will always be home by midnight, the "Mobilis" day pass, which allows unlimited transport on Bus and Metro/RER, is a daily pass which is priced according to the zones you'll be travelling in. Might be worth your while if you're staying within central Paris, which covers Zones 1 + 2 and costs 7 EU per day.
Both these ticket options can be purchased in Metro stations using the machines or at manned booths with the word "VENTE" above.
Though the other passes you mentioned give slight discounts on some attractions, I think they're over-priced for what they offer.
